The Coordinate Manipulation Commands
The commands in this section are primarily used for moving
some or all of the atoms. There is a wide range of commands and options.
All of the commands may be used on either the main coordinate set, or
the comparison set. Some commands require both sets of coordinates.
* Menu:
* Syntax:: Syntax of the coordinate manipulations commands
* Simple:: Descriptions of the simple commands
* Function:: Descriptions of the remaining commands
* Substitutions:: Description and usage of substitution values
Syntax of Coordinate Manipulation commands
[SYNTAX COORdinate manipulation]
COORdinates { INITialize } [COMP] [atom-selection]
{ COPY } [WEIGhting_array]
{ SWAP } [IMAGes]
{ AVERage [ FACT real ] }
{ SCALe [ FACT real ] }
{ MASS_weighting }
{ ADD }
{ SET vector-spec }
{ TRANslate vector-spec }
{ ROTAte vector-spec {PHI real} }
{ {MATRix} }
{ TWISt vector-spec RATE real }
{ ORIEnt [MASS] [RMS] [NOROtation] }
{ RMS [MASS] }
{ DIFFerence }
{ FORCe [MASS] }
{ SHAKe [MASS] }
{ DRAW draw-spec }
{ DISTance distance-spec [DIFF] }
{ DIPOle [OXYZ] [MASS] }
{ MINDist distance-spec }
{ MAXDist distance-spec }
{ READ io-specification }
{ WRITe io-specification }
{ PRINt io-specification }
{ RGYR [MASS] [FACT <real>] }
{ OPERate image_name }
{ STATistics [MASS] }
{ VOLUme {SPACe integer} }
{ }
{ DUPLicate { 2X(atom-selection) } }
{ { PREVious } }
COORdinates HISTogram { X } [IUNIt int] HMIN real HMAX real HNUM integer -
{ Y } [HSAVe] [HPRInt] [HNORm real] [HDENsity real] -
{ Z } [COMP] [WEIGhting_array] atom_selection
{ R }
COORdinates { HBONd } [CUTHB <real>] [CUTHA <real>] [IUNIt <int>] -
{ CONTact } [BRIDge <resnam>] [VERBose] [TCUT real] -
2X(atom-selection) traj-spec -
[IRHI <int> [DRH <real> ][RHMAx <real>] ] -
[ITHI <int> [DTH <real> ][THMAx <real>] ]
COORdinates DYNAmics [COMParison] [PAX] [atom-selection] [NOPRint] -
traj-spec [ORIENT [MASS] [atom-selection] ]
COORdinates PAXAnalysis [COMParison] [atom-selection] [NOPRint] [SAVE] -
traj-spec
COORdinates SEARch { search-spec } disposition-spec
{ INVErt }
{ KEEP xvalue yvalue zvalue }
{ EXTEnd RBUFf real }
search-spec :: [atom-selection] [COMP] [IMAGe] [operation-spec]
[XMIN real] [XMAX real] [XGRId integer]
[YMIN real] [YMAX real] [YGRId integer]
[ZMIN real] [ZMAX real] [ZGRId integer]
operation-spec ::= { } { [VACUum] } { [RESEt] }
{ [RCUT real] } { FILLed } { AND }
{ [RBUFf real] } { HOLES } { OR }
{ XOR }
{ ADD }
disposition-spec::= { [NOPRint] } [NOSAve] [CREAte segid CHEM type]
{PRINt [UNIT int]} [ SAVE ]
COORdinates SURFace [atom-selection] [WEIGhting] { CONTact-area }
[ACCUracy real] { ACCEssible-area }
[RPRObe real]
COORdinates CONVert-from/to-unit-cell [ from | to ] -
[atom-selection] [COMP] [IMAGe] -
a b c alpha beta gamma
[ from | to ] ::= [ FRACtional | SYMMetric | ALIGned ]
COORdinates AXIS atom-selection [atom-selection] [MASS] [COMP] [IMAGEs]
COORdinates LSQP [ NORM ] [VERBose] [MASS] [COMP] [IMAGEs] [WEIGh] -
[ MAJOr ]
[ MINOr ]
atom-selection
COORdinates COVAriance traj-spec 2x(atom_selection) [UNIT_for_output int] -
[RESIdue_average_nsets integer] [MATRix] -
[ENTRopy [TEMP <real>] [DIAG] [RESI] [SCHL] ]
COORDinates DMAT -
[RESIdue_averaging] [NOE_weighting] [SINGle_coordinate_file] -
[CUTOff <real>] [UNIT_for_output <int>] [TRAJectory] [CUTOff <real>] -
[PROJect UPRJ <int>] [PROBability UPRB <int>] [TOLE <real>] MKPRoj -
traj-spec 2x(atom_selection) [ [RELAtive] RMSF [DUNIt <int>]] [MATRix]
COORdinates PUCKer [SEGId segid] RESId resid1 [TO resid2] [AS | CP]
COORdinates HELIx atom-selection [atom-selection]
COORdinate ANALysis {WATer} [RLP <int>] <atom-selection> -
{XREF <real> YREF <real> ZREF <real>} - ! setup arbitrary analysis point
{CROSs|SITE [MULTI] <atom-selection>} - ! setup solute analysis site or
! cross terms for arbitrary solvent
traj-spec - ! reading trajectories
NCORs <int> RSPIn <real> RSPOut <real> - ! MSD/IVAC set-up
RSPHere <real> DR <real> MGN <int> - ! g(r) setup
RDSP <real> - ! cutoff for DENS,KIRK and DBF
DENS <real> - ! userspecified bulk density
! (atoms/A**3)
! for normalization of g(r)
{IMSD <unit>|IVAC <unit>} IDENs <unit> - ! output for MSD, VAC and DENsity
{IGDISt <unit> [IHH <unit>] [IOH <unit>]|ISDISt <unit>} - ! g(r) requests
{BYGRoup|BYREsidue|BYSEgment} ! discard distances WITHIN
! specified unit for g(r)
IMRD ! Magnetic Relaxation Dispersion analysis
RRES cutoff radius for calculation of residence time. if 0 use shell
beteween RSPIN, RSPOUT
IKIRkg <unit> - ! Kirkwood g-factor (dipole correlations)
RKIRk ! distance dependent Kirkwood factor for water
! iff a SITE MULTI selection containing at least two atoms is
given, then a unit-vector pointing from the first to
the second site atoms will be used in the
scalar product with a unit vector along the water dipoles
NKIRk number of points in r-dimension for IKIR and RKIR
from r=0 to r=RDSP
XBOX <real> YBOX <real> ZBOX <real> - !PBC info for analysis
IFDBF <unit> IFDT <unit> RCUT <real> ZP0 <real> NZP <int> - ! DBF analysis
IHIST <unit> IPDB <unit> [XMIN <real> XMAX <real> DX <real>] - !3D histogram
[YMIN <real> YMAX <real> DY <real>] -
[ZMIN <real> ZMAX <real> DZ <real>] -
[WEIGht] [CHARge] [DIPOle] -
[THREshold <real>] [NORM <real>] -
IDIP <unit> [MIND <real>] [MAXD <real>] [NUMD <int>] -
! dipole distribution
EXVC <atom-selection> MCP <int> MCSH <int> - ! EXcludedVolumeCorrection
RPRObe <real> ISEEd <int> -
RCOR <integer> - ! Rotational Correlation Time Analysis
ROUT <unit> TLOW <real> TUP <real> MAXT <integer> -
IHYDn <integer> RHYD <real> ! Hydration numner
COORdinates INERtia [atom-selection] -
[ENTRopy [TEMPerature <real>] [SIGMa <real>] ]
atom-selection:== (see *note select:(select.doc).)
distance-spec::=
{ WEIGhting vector-spec atom-selection }
{ }
{ [UNIT int] [CUT real] [ENERGy [CLOSe]] 2X(atom-selection) - }
{ [Nonbonds] } { [NO14exclusions] } { [NOEXclusions] } -
{ NONOnbonds } { 14EXclusions } { EXCLusions }
[TRIAngle] [ HISTogram HMIN real HMAX real HNUM integer -
[HSAVe] [HPRInt] [HNORm real] [HDENsity real] ]
vector-spec::= { [XDIR real] [YDIR real] [ZDIR real] } [DISTance real]
[XCEN real] [YCEN real] [ZCEN real] [FACTor real]
{ AXIS }
draw-spec::= [DFACt real] [NOMO] UNIT integer
io-specification:== (see *note io:(io.doc).)
traj-spec::= [FIRSt int] [NUNIts int] [NSKIp int] [BEGIn int] [STOP int]
Descriptions of the simple coordinate manipulation commands
All of these commands allow either the main coordinate set (default),
or the comparison set (COMP keyword) to be modified. The other coordinate
set is only changed by the SWAP command and the ORIEnt RMS command when
the specified atoms are not centered about the origin.
Each of these commands may also operate on a subset of the full
atom space. The selection specification should be at the end of the command.
The default atom selection includes all atoms.
If the IMAGes keyword is specified, then the operation will be
performed on the image atoms as well (if images are present).
------------------------------------------------------------------------------
1) The INITialize command
The INITialize command returns the coordinate values of the
specified atoms to their start up values (9999.0). The main use of
this command is in connection with the IC BUILD command, which may
only find coordinates for atoms with the initial value.
------------------------------------------------------------------------------
2) The COPY command
The COPY command will copy the coordinate values into the
specified set FROM the other coordinate set.
------------------------------------------------------------------------------
3) The SWAP command
The SWAP command will cause the coordinate values of the
specified atoms to be swapped with the comparison set.
------------------------------------------------------------------------------
4) the AVERage command
The AVERage command will generate a new coordinate set at a
point along the displacement vector between the present coordinate set
and the other set. The FACTor value determines the relative step along
this vector. Its default value is 0.5 (a true average). A FACTor value of
1.0 is equivalent to the copy command. Negative or greater than unit
positive values are also allowed.
------------------------------------------------------------------------------
5) The SCALe command
The SCALe command will cause the coordinate values for all
selected values to be scaled by a required scale factor. This option
is designed to work with coordinate displacement vectors. A scale
factor of zero will set the selected coordinate values to zero.
This option may also be useful in plotting.
------------------------------------------------------------------------------
6) The MASS_weighting command
The MASS_weighting command will cause all selected coordinates
to be scaled by the MASS of each atom. If the WEIGht option is specified,
the weighting array will be scaled.
------------------------------------------------------------------------------
7) The ADD command
The add command will add the main and the comparison
coordinate values and store the results in the selected coordinate set.
As with other commands, only selected atoms will be modified. If
an atom in either set is undefined, then the sum will also be undefined.
This option is designed for use in cases where one or both coordinate
sets contain coordinate displacement vectors.
------------------------------------------------------------------------------
8) The SET command
The SET command will set all coordinate values of selected
atoms to a specified value determined by the vector specified. This is
a simple manner in which to zero a coordinate set with the command;
COOR SET XDIR 1.0 DIST 0.0
Note, the XDIR keyword value was included so that the vector has a nonzero
norm (required for all vector specifications).
------------------------------------------------------------------------------
9) The TRANslate command
The TRANslate command will cause the coordinate values of
the specified atoms to be translated. The translation step may be
specified by either X,Y, and Z displacements, or by a distance along
the specified vector. When no distance is specified, The XDIR,YDIR, and
ZDIR values will be the step vector. If the AXIS keyword is used, then
the translation will be along the axis defined by the previous COOR AXIS
command. For this option, a distance may be specified, but if it isn't,
then the translation distance will be the COOR AXIS vector length
------------------------------------------------------------------------------
10) The ROTAte command
The ROTAte command will cause the specified atoms to be rotated
about the specified axis vector through the specified center. The vector
need not be normalized, but it must have a non-zero length. If the AXIS
keyword is used, then the axis and center information from the last
COORdinates AXIS command will be used. The PHI value gives the amount
of rotation about this axis in degrees.
Only the atoms specified will be rotated. If the MATRix keyword is used
the rotation will be made using an explicit rotation matrix, input in
free format on the three following lines (3 real numbers /line):
U(1,1) U(1,2) U(1,3)
U(2,1) U(2,2) U(2,3)
U(3,1) U(3,2) U(3,3)
NOTE: This command uses a LEFT HAND sense, not the usual right hand rule...
It was a mistake, but this is kept for historical reasons (numerous scripts).
The left hand sense is consistent with dihedral angles (i.e. if you define a
vector along bond A-B (from A to B) and then rotate B (and its bonds) by a
positive angle (in the left hand sense), then the dihedral angles will
increase. Other rotation angles in CHARMM (should) use the regular
right hand rule (except for the COOR TWISt command).
------------------------------------------------------------------------------
10.5) The TWISt command
The TWISt command will cause the specified atoms to be rotated
about the specified axis vector through the specified center. The vector
need not be normalized, but it must have a non-zero length. If the AXIS
keyword is used, then the axis and center information from the last
COORdinates AXIS command will be used. The amount of rotation will depend
on the projected distance of the atom on the axis multiplied by the RATE
value (in degrees).
This command was designed to generate helical structures that are more or
less twisted than an initial helical structure. This is an easy way to
homogeneously perturb a helix. I can be also used to induce a twist in
planar structures.
NOTE: this command uses a left handed sense, not the usual right hand rule...
(see ROTAte above).
------------------------------------------------------------------------------
11) The ORIEnt command
The ORIEnt command will modify the coordinate values of ALL of
the atoms. The select set of atoms is first centered about the origin,
and then rotated to either align with the axis, or the other coordinate set.
The RMS keyword will use the other coordinate set as a rotation reference.
The MASS keyword cause a mass weighting to be done. This will
align the specified atoms along their moments of inertia. When the RMS
keyword is not used, then the structure is rotated so that its principle
geometric axis coincides with the X-axis and the next largest coincides
with the Y-axis. This command is primarily used for preparing a
structure for graphics and viewing. It can also be used for finding
RMS differences, and in conjunction with the vibrational analysis.
The NOROtation keyword will suppress rotations. In this case,
only one coordinate set will be modified.
------------------------------------------------------------------------------
12) The RMS command
The RMS command will compute the RMS or mass weighted RMS
coordinate differences between the selected set of atoms just as they
lie. This differences from the COOR ORIENT RMS command in that no coordinate
modifications are made and no translation is done.
------------------------------------------------------------------------------
13) The DIFF command
The DIFF command will compute the differences between the main
and comparison set (or the reverse) and store this difference in the
modified coordinate set. Undefined or unselected atoms result in a zero.
If the WEIGht keyword is invoked, then the WCOMP array is subtracted from
WMAIN and the coordinates are untouched.
------------------------------------------------------------------------------
14) The FORCe command
The FORCe command will copy the current forces (DX,DY,DZ)
of the selected atoms to the specified coordinate set. Atoms not selected
are given a value of zero. If the MASS keyword is specified, then the
forces will be divided by the mass. This would correspond to an
acceleration in dynamics.
------------------------------------------------------------------------------
15) The SHAKe command
This command will SHAKE the selected coordinate set with respect
to the other (as a reference). A mass weighting may be used. Any atoms
that are not selected are considered to be fixed (infinite mass).
In order to use this command, the SHAKe command must first be invoked
which sets up the shake constraints.
------------------------------------------------------------------------------
16) The DIPOle command
Calculates the dipole moment of selected atoms. If total charge
is not zero, the dipole moment is somewhat ill-defined and coordinate system
dependent; in this case the center of geometry of the selected atoms is used
as origin for the coordinate system in which the dipole moment is calculated.
This can be altered by the MASS keyword. If it is present the center of mass
will be used as origin of the relative coordinate system.
For the purpose of compatibility with Gaussian program this feature can be
disabled by adding OXYZ keyword, which forces calculation of dipole moment
relatively to the origin of Cartesian coordinate system.
Prints out dipole moment cartesian components and magnitude (in Debyes) and
the total charge. CHARMM variables ?CHARGE, ?XDIP, ?YDIP, ?ZDIP, and ?RDIP
(charge, x,y,z and magnitude of dipole) are set.
Descriptions of the remaining corman commands
See the descriptions of the simple commands for some background
information on these commands.
------------------------------------------------------------------------------
1) The DISTance command
The COOR DIST command will either find distances between atoms
or the distances of atoms from a fixed point in space (WEIGh option).
This command can find distances within a single coordinate set, or
find distances between atoms in two coordinate sets (DIFF option).
The DISTance command can find all atom distances between two
atom selections. A unit number may be specified (default=6) and a
cutoff distance may be included as well (default=8999.0). If no selection
is specified, all atoms will be included! The delimiter ENDselection
must separate the two sets of atom selections. The van der Waal energy
may be requested with the "ENERgy" keyword, and if this option is used,
the list of pairs with a positive van der Waal energy may be selected
with the "CLOSe" keyword (i.e. only close contacts will be listed).
The NEAR option will list the nearest atom in the second atom selection
to the atoms in the first selection.
The COOR DISTance command doesn't gives distances between
excluded atoms unless the "EXCLusions" keyword is specified. This make
it much easier to search for bad contacts. Likewise, 1-4 interactions and
other interactions may be requested or omitted.
The command;
COOR DISTance ENERgy CLOSe CUT 5.0 SELE ALL END SELE ALL END -
14EXclusions NONBonds
will list all atom pairs that have a positive van der Waal energy.
The command;
COOR DISTance ENERGY CUT 5.0 NONONbonds NOEXclusions 14EXCLusions -
SELE ALL END SELE ALL END
will list all 1-4 interactions and energies (and nothing else).
The command;
COOR DISTance ENERgy CUT 4.5 SELE RESID 23 END SELE ALL END
will list all contacts less than 4.5A that residue 23 has with the rest of
the system without considering 1-4 interactions or excluded pairs.
The 1-4 vdw terms, E14FAC, and EPS values other than 1.0 are recognized.
The WEIGht option puts the distance of all selected atoms from some
specified point. If no point is specified, then the origin is used. This
is most useful in computing magnitudes of forces or coordinate differences.
For example, the sequence;
ENERGY ...
COOR FORCE COMP ! copy forces to the comparison coordinates
COOR DIST WEIGH COMP ! put magnitudes in the weighting array.
PRINT COOR COMP SELE PROP WCOMP .GT. 5.0 END ! print atoms with large
forces. Note that all operations were done on the comparison set.
The DIFF keyword causes the selection to work on different coordinate
sets, where the first selection corresponds to the set specified (MAIN or
COMP), and the second atom selection uses the other coordinate set.
The HISTogram option allows a histogram of distances to be produced.
With the histogram, the HMIN and HMAX (the range of the histogram in angstroms)
and the HNUM (the number of bins) must be specified. The HSAVe keyword causes
the histogram values to be saved for subsequent COOR DIST commands. In a loop,
this allows g(r) to be calculated from a dynamics trajectory. The HPRInt
option will cause the final histogram values to be printed. The HNORm value
will be used to normalize the histogram before printing (divide by HNORm).
A density value, HDENS, is also required, which is the number of selected
objects divided by the volume per object. Also note: In order to get
this to work with with the crystal facility, the first atom selection
(in the loop) should only include primary atoms, and the second atom
selection should include both primary and image atoms.
The histogram will be scaled by the reciprocal of the distance squared
The histogram will also be scaled by the reciprocal of the distance squared
(to get normalized g(r) plots). Three columns of numbers are output;
(1) the bin midpoint distance, (2) the normalized g(r), and (3) the total
number of pairs within the bin divided by the HNORM value.
A PRNLEV less than 5 will suppress the listing of distance pairs.
Example of use to get a distance distribution plot:
update imgfrq 20 cutim 20.0
traj ....
prnlev 4
set 1 1
label loop
traj read
update inbf 0 IMALL cutim 10.5
coor dist image sele segid main .and. type OH2 end sele type OH2 end -
cut 10.5 HIST HMIN 0.0 HMAX 10.0 HNUM 50 HSAVE
incr 1 by 1
if 1 .lt. 1000.5 goto loop
calc dens = 216.0/30.0 ! #waters/(volume/water)
coor dist sele none end sele none end -
cut 10.5 HIST HMIN 0.0 HMAX 10.0 HNUM 50 HNORM 1000.0 -
HPRINT HDENS @dens
------------------------------------------------------------------------------
2) The RGYR command
The RGYR command can compute the Radius of GYRation, center-of-mass
and total mass of the specified atoms. By default the RGYR, uses a unit
weighting factor providing the rms distance from the center of geometry.
The current keywords are:
MASS use mass weighting (otherwise use unit weight per selected atom)
WEIG use a weight array (WMAIN or WCOMP) for the weighting
FACT constant to be subtracted from each weight
The weight arrays can be filled, by using COOR or SCALAR commands,
before invoking the RGYR routine. In this way almost any RGYR can be computed.
------------------------------------------------------------------------------
3) The LSQP command
The LSQP command computes the least-squares-plane through the
selected atoms. Weighting can be done by the atom masses [MASS], by
the weighting array [WEIG], or not at all (default). Output is the
equation for the plane, the sum-of-squared distances (weighted) from
the plane (SSQ), and the center-of-mass of the selected atoms.
The keyword VERBose causes some additional output, most useful of
which is the distance from the plane for each atom.
The options; NORM, MAJOr, and MINOr select which vector is
stored as the AXIS (see COOR AXIS command for more details). The default
is to not set the AXIS variables.
------------------------------------------------------------------------------
4) The OPERate command.
The OPERate command processes the selected coordinates through
the image transformation specified by name. This command may only be
used if an image file has been read. The image_name is one of the
image transformation names (WRITE IMAGE TRANS). This is also the SEGID
of the image atoms created by the image update procedure.
------------------------------------------------------------------------------
5) The MINDistance command.
The MINDistance command computes the minimum distance between
selected coordinates. Usually this command is executed with a double
selection. Note that the default distance-spec excludes bonded atoms and 1-4
interactions. If only one selection is given, then it will give the minimum
distance of the selected coordinates between the MAIN and COMPARISON set.
------------------------------------------------------------------------------
6) The MAXDistance command.
The MAXDistance command computes the maximum distance between
selected coordinates. This command is executed with a double selection.
------------------------------------------------------------------------------
7) The STATistics command
The STATistics command will print some simple statistics
regarding the selected atoms. The values XMIN,YMAX,XAVE,YMIN,YMAX,YAVE,
ZMIN,ZMAX,ZAVE,WMIN,WMAX,WAVE are set when this command is executed. These
variable values may then be used un subsequent commands with the "?" symbol.
For example, the command sequence may be used to shift a structure so that
a single atom is in the X-Y plane (e.g. shift in the z-direction);
COOR STATistics SELE desired-atom END
COOR TRANS ZDIR ?ZAVE FACT -1.0
The MASS option will place the average values at the center of mass.
------------------------------------------------------------------------------
8) The AXIS command.
The AXIS command generates a vector and saves it for subsequent use
for either command parsing, or for use as input in the COOR SET, COOR ROTAte,
COOR TRANslate, or COOR DISTance WEIGhting commands by using the AXIS keyword.
There are two modes for the AXIS command. With a single atom selection, the
stored vector is the defined from the origin to the center of geometry/mass
of all selected atoms. With two atom selections, the vector spans from the
center of the first set of selected atoms to the center of the second.
The MASS keyword invokes the usage of the center of mass.
The AXIS command sets the variables XAXIs, YAXIs, ZAXIs, RAXIs, XCEN, YCEN,
and ZCEN, which may be accessed with the "?" symbol. These values define
the actual vector, the length of the vector, and the center of the vector
(midpoint). For example, to use the distance between two atoms as a
criterion to terminating a run, the following command sequence could be used;
SET 1 10.0
COOR AXIS SELE first-atom END SELE second-atom END
IF 1 GT ?RAXIs STOP
For another example, to rotate the chi-1 torsion of a
specified residue BY 30 degrees, the command sequence would be appropriate;
DEFINE BACK SELE TYPE O .OR. TYPE N .OR. TYPE H .OR. TYPE CA .OR. TYPE C END
COOR AXIS SELE ATOM MAIN 23 CA END SELE MAIN 23 CB END
COOR ROTATE AXIS PHI 30.0 SELE RESID 23 .AND. .NOT. BACK END
------------------------------------------------------------------------------
9) The DUPLicate command.
The DUPLicate command copies coordinates between atoms within
a structure. The coordinates are copied FROM the first selection TO the
second selection. If the selections overlap, watch out!. The matching is
done by number within the selected coordinate sets. If the two selection
have a different number of atoms, a warning will be issued, and the smaller
number will be used. For example, if one needs to compute the relative
orientation between two alpha helicies, the following input might be used;
COOR COPY COMP
COOR DUPL COMP SELE backbone of first END SELE backbone of second END
COOR ORIE RMS MASS COMP SELE backbone of second END
This will give the RMS shift between these helicies as well as the
coordinate transformation required to map one into the other.
The PREVious option may be used with a single atom selection.
This assigns the coordinate position of selected atoms to the value
of the previous atom (by number). This has been used with the command;
COOR DUPLicate PREVious SELE TYPE H* END
to assign hydrogen atom positions to that of the associated heavy atom.
The COMP keyword causes only the comparison coordinates to be used and
modified. Otherwise, the entire operation involves only the main coordinates.
------------------------------------------------------------------------------
10) The DYNAmics command
The COOR DYNAmics command will read a (set of) dynamics trajectory
files and compute the average coordinates (stored in the selected
coordinate set) and the isotropic rms fluctuations (stored in the weighting
array). The first unit number (FIRSt)(default 51), number of units (NUNIts)
(default 1), frequency of accepted coordinate sets (NSKIp)(default 1),
starting set (BEGIn)(default first set), last set (STOP)(default last set),
may be specified. Option values are not remembered with subsequent
COOR DYNA commands. The NOPRint supresses much of the output.
If the keyword ORIENT is present, all coordinate frames will be
RMS re-oriented with respect to the COMParison set (must be defined);
if the word MASS is also there the coordinates will be mass-weigthed for
re-orientation; if a second atom selection is provided, only those selected
atoms will be used.
The PAX command causes the Principal AXis of the motion of each atom
to be computed and save. The print out gives the direction and magnitude
of the fluctuation as well as the anisotropies. The PAX data is saved for
a subsequent COOR PAXAnal command if further analysis is desired.
------------------------------------------------------------------------------
11) the PAXAnal command
The COOR PAXAnal command computes additional data regarding the
Pricipal AXis data (computed by the most recent COOR DYNA PAX command).
The trajectory must be reopened and reread, or a different trajectory
may be substituted. This command prints data for each selected atom and
averages over the selected atoms. The printout includes the skew and
kurtosis, anisotropies, as well as all of the low moments of the motion.
The SAVE option causes the PAX data structure (from the COOR DYNA PAX command)
to be saved (for subsequent COOR PAXA commands).
------------------------------------------------------------------------------
12) the SEARch command
COORdinates SEARch { search-spec } disposition-spec
{ INVErt }
{ KEEP xvalue yvalue zvalue }
{ EXTEnd RBUFf real }
search-spec :: [atom-selection] [COMP] [IMAGe] [operation-spec]
[XMIN real] [XMAX real] [XGRId integer]
[YMIN real] [YMAX real] [YGRId integer]
[ZMIN real] [ZMAX real] [ZGRId integer]
operation-spec ::= { } { [VACUum] } { [RESEt] }
{ [RCUT real] } { FILLed } { AND }
{ [RBUFf real] } { HOLES } { OR }
{ XOR }
{ ADD }
disposition-spec::= { [NOPRint] } [NOSAve] [CREAte segid CHEM type]
{PRINt [UNIT int]} [ SAVE ]
The SEARch command generates and/or manipulates a grid of small volume
elements.
The SEARch command will search through a set of grid points
for vacuum space points (i.e. points outside the van der Waal radius of
any atom). In the default mode (NOPRint), only the relative volume of filled
and vacuum points are printed concerning the selected atoms.
The grid specifiers must be input (min, max, and grid) for each dimension.
(grid implies number of grid points. Hence
XMIN -10.0 XMAX 10.0 XGRID 41
implies a half Angstrom sampling along the x direction)
The FILLed option will cause non-vacuum points to be listed or plotted.
The PRINt option will cause all found grid points to be listed on the
output unit specified (default 6).
For this command, the atom sizes (radii) are taken from the weighting
array. To get van der Waal radii into the weighting array, the command;
SCALar WMAIn = RADIus
may be used. If a hole big enough to stuff a water into is to be found,
then the command sequence;
SCALar WMAIn = RADIus
SCALAR WMAIN ADD 1.6
SCALAR WMAIN MULT 0.85
would be probably the best to use.
If the RCUT or RBUFf value is set to a nonzero value, then the accessible
volume command is enabled. When RCUT is set, this is the maximum radius.
When RBUFf is set, then the maximum radius is the weighting array plus the
RBUFf value. The weighting array is returned with the fraction of free volume
in the shell from the atom radius to the maximum radius.
If the HOLEs keyword is set, only the grid points not connected to the
first point (point in the negative corner of the box) are considered.
In this way, the volume of just the holes can be analyzed and saved.
The "ADD" option for the COOR SEARCH command has been added to allow
the calculation of partial occupancy factors. This allow holes in proteins
to be analyzed for flexibility and variability.
It is possilbe to use multiple COOR SEARch commands and to use boolean
operations to combine the results. For example, the script sequence;
COORdinates SEARch IMAGe -
XMIN -10.0 XMAX 10.0 XGRId 20 -
YMIN -10.0 YMAX 10.0 YGRId 20 -
ZMIN -10.0 ZMAX 10.0 ZGRId 20 -
NOPRINT VACUUM SAVE
....
SCALAR WMAIN ...
....
COORdinates SEARch IMAGe -
XMIN -10.0 XMAX 10.0 XGRId 20 -
YMIN -10.0 YMAX 10.0 YGRId 20 -
ZMIN -10.0 ZMAX 10.0 ZGRId 20 -
AND PRINT UNIT 22 RBUFF 2.0 FILLED NOSAVE
Note, the results of these two commands are computed and the
intersection (AND) is printed. The first command needs a "SAVE" in order
for the results to be saved. Also, the grids (if specified) must exactly match
(same number of grid points in all dimensions) for this operation to work.
The COOR SEARch command allocates space, if needed, and frees the space when
the NOSAve option is used. Thus, if four COOR SEARch commands are needed for a
single computation, the first must have the SAVE option. The only way
to free the space allocated by the COOR SEARch SAVE command is to run another
COOR SEARch command with the NOSAve option.
If the CREAte option is used then the specified grid points will be
added to the PSF as dummy atoms. The chemical type of the dummy atom must
be specified and it must be present in the current RTF. This option can be
used for graphics or for other hole analysis (shape,...). This option
will add one segment to the PSF, one residue and atoms and groups equal to
the number of selected grid points.
------------------------------------------------------------------------------
13) the VOLUme command
The VOLUme command will compute the volume of a selected set of
atoms. Its operation is the same as that of the SEARch command, except
that only the volume is printed and the degree of exposure for each atom
is returned in the weighting array. The SCALAR storage arrays must be filled
before using this command. The first storage array [1] must contain
the radii of each atom (RMIN) and the second storage array must contain the
outer probe distance (RMAX) for each atom. The free volume within the RMIN
to RMAX range and not within RMIN of any other atom will be returned in the
weighting array as a ratio of the maximum possible value. For example a
completely exposed atom will return a value of 1.0 and an atom in the interior
of a protein would return a value of 0.0. The HOLEs keyword feature
causes holes within the selected atoms to be filled before computing
the total volume and the accesible volume.
SPACE is a maximum number of cubic pixels
i.e. SPACE = x_points * y_points * z_points
Larger SPACE value results in more accurate calculation but it takes more
memory an computer time. Number of points in x,y and z directions are
determined according to the formula:
factor = ( SPACE / (a*b*c) ) ** (1/3)
x_points = factor*a
y_points = factor*b
z_points = factor*c
where a, b and c are dimensions of the smallest rectangular box
enclosing the molecule.
------------------------------------------------------------------------------
14) The SURFace command
The COOR SURFace command computes the Lee and Richards surface for
selected atoms and stores the result in the appropriate weighting
array. If the "WEIGhting" keyword is used, the radii are obtained from
the weighting array (and then written over), otherwise the radii are
obtained from the parameter file values. The radius of the probe may
be specified (default 1.6) and the accuracy may be specified (default 0.05).
Either ACCEssible surface (default) or CONTact surface may be specified.
Contact surface is equivalent to Accessible surface if a zero probe
radius is used. If the accuracy is not specified (or set to zero), then
the analytic result is provided. If a nonzero accuracy is provided,
then the original Lee and Richard's (points on a sphere) algorithm
is used.
------------------------------------------------------------------------------
15) The HELIX command
The COOR HELIx command will analyze a single helix, or the relative
orientation of two helices. The use this command, one or two atom
selections should be provided selecting ONLY the atoms which will be
used to define the helix. The order of these atoms is important.
With a single atom selection, this command calculates the normalized
axis (A) and the perpendicular vector (R0) from the origin to A of
the cylinder most closely approximating a helix on which the selected
atoms best fit (Algorithm by J. Aqvist Computers & Chemistry
Vol. 10, pp97-99, (1986)).
With a double atom selection, this command also computes helix
axis and helix-helix structure analysis (Algorithm by Chotia, Levitt, and
Richardson JMB 145, P215-250 (1981)).
------------------------------------------------------------------------------
16) The CONVert command
The COOR CONVert command will cause the coordinates of all
defined and selected atoms to be transformed from the unit cell to
cartesian coordinates or back from cartesian to fractional coordinates.
Two orientations in cartesian coordinates are supported :
ALIGned - in which b-vector is along y-axis and a-vector
in xy-plane (this is old charmm standard)
SYMMetric - in which shape matrix constructed from unit
cell vectors is symmetric
Two keywords in any order [FRAC|ALIG|SYMM] are required after CONVert.
Unit cell parameters (a,b,c,alpha,beta,gamma) follow in the same line.
The angle values are specified in degrees. See the routine CONCOR for
details concerning the transformation.
As an example, the following manipulations should have no net affect on the
coordinates,
COOR COPY COMP
COOR CONVERT SYMMETRIC FRACTIONAL 5.6 12.2 5.4 80.0 95. 100.
COOR CONVERT FRACTIONAL SYMMETRIC 5.6 12.2 5.4 80.0 95. 100.
COOR CONVERT SYMMETRIC ALIGNED 5.6 12.2 5.4 80.0 95. 100.
COOR CONVERT ALIGNED FRACTIONAL 5.6 12.2 5.4 80.0 95. 100.
COOR CONVERT FRACTIONAL ALIGNED 5.6 12.2 5.4 80.0 95. 100.
COOR CONVERT ALIGNED SYMMETRIC 5.6 12.2 5.4 80.0 95. 100.
COOR DIFF
COOR STAT
When working with a triclinic system, the user should be aware of the form
of the coordinates. Most of the data from crystallography is in fractional
(coordinates between zero and one) or in the aligned frame.
NOTE: All of the internal use in CHARMM for energy calls, minimization,
or dynamics ASSUMES that the coordinates are in the symmetric frame.
------------------------------------------------------------------------------
17) The COVAriance command
The covariance command under coordinate manipulations
computes covariances of the spatial atom displacements of
a dynamics trajectory for selected pairs of atoms.
mu = E[ (R - E[R ]) (R - E[R ] )
JK J J K K
= E[R R ] - E[R ] E[R ]
J K J K
and the normalized covariance matrix is given by
CO = mu / SQRT(mu mu )
JK JK JJ KK
The command syntax and varibles are as in the coor dynamics command.
The exceptions are the keywords:
SET1: specifies the selection for the "J" groups in covariance
SET2: specifies the selection for the "K" groups in covariance
UNIT_for_output: specifies unit for output of covarience matrix (ascii)
RESIdue_average: is a logical for computing the average over
residues in SET2 specification. When followed by
NSETS: equal to 2 the average is over both SET1 and SET2
giving a NRES1 x NRES2 covariance matrix.
MATRix gives output of just the covariance values in a matrix format
ENTRopy config. entropy [kcal/mol/K] using approximation S'' of
Andricioaei&Karplus (J. Chem. Phys 115,6289 (2001)) or
SCHL J. Schlitter's variation S'
(Chem. Phys. Lett. 215, 617 (1993)) on Karplus&Kushick.
See also Schafer et al J. Chem. Phys. 113, 7809 (2000).
This approximation is an upper limit to the true entropy.
Sets CHARMM variable ENTROPY
It is recommended to remove translational(rotational) motion
before extracting the entropy (merge orient..[norot].);
for flexible molecules removal of rotation may be tricky.
NB! The covariance matrix used for this calculation is
not normalized and is 3N by 3N
TEMP temperature used in entropy calculation (default 298.15)
DIAG use only diagonal elements of covariance matrix,
mainly for testing purposes
RESI evaluate entropy using covariance for each residue only
Example:
!Get configurational entropy at T=300K and save the unnormalized covariance
!matrix, using all atoms in the PSF
coor cova firstu 51 nunit 1 entropy matrix unit 61 temp 300.0
! Same without saving or printing the matrix and with output for each residue
coor cova firstu 51 nunit 1 entropy unit -1 temp 300.0 resi
------------------------------------------------------------------------------
18) The DMAT command
This command is accessed with the command COOR DMAT and provides some
general tools for the calculation, manipulation and storage/extraction of
distance matrix based properties. This routine has some overlap with the
new distance command introduced by Bernie Brooks but also provides significant
complementarity in extending the range of properties computed.
The entire syntax is:
[SYNTAX]
COORdinates DMAT -
RESIdue_average NOE_weighting -
SINGle -
FIRSt_unit <int> NUNIt <int> BEGIn <int> SKIP <int> -
STOP <int> 2x<atom selection (SET1, SET2)> -
UNIT_for_output <int> TRAJectory CUTOff <real> -
PROJect UPRJ <int> [MKPRoj] PROBability UPRB <int> TOLE <real> -
[ [RELAtive] RMSF] [DUNIt <int>] [MATRix]
The command structure is like that of most other coordinate manipulation
commands other sub-parser keywords are:
UNIT the distance matrix will be written to the unit
number specified as an ASCII file unless the TRAJ
keyword is specified, in which case a binary "trajectory" of
the distance matrix will be written.
RESIdue this keyword specifies to compute the distance matrix
for a center of geometry weighted average of residues
NOE this keyword denotes that the averaging over distances
in the distance matrix should be inverse sixth power
weighted.
TRAJ write a dynamic trajectory file of the distance matrix
SINGle process only a single coordinate file
CUTOff print only those values of the distance matrix which are
smaller than cutoff value
PROJect project out a subset of contacts for printing
UPRJ read projection matrix from unit UPRJ
MKPRoj A projection matrix will be printed. Its elements are 1 if
the distance is < CUTOff, 0 otherwise. To be used with subsequent
PROJ UPRJ unit command. (If a standard DMAT is used as projection
matrix the CUTOff in the PROJ command has to be squared)
PROB compute the contact probability based on differences
from reference contact map read from UPRB and with
an upperbound tolerance of TOLE
RMSF Computes the root mean square fluctuation in the distance
matrix from the trajectory. Disables the printing of
the binary file.
RELAtive Divides the RMSF value by the distance
DUNIt Write distances to file open on the specified unit. This
allows calculation of distance and (relative) fluctuation
matrices in one pass.
MATRix Output is in the form of a rectangular matrix with just the
z-values (distances or fluctuations)
Note: The binary file produced is analogous to the binary trajectory files and
contain the following information:
WRITE(UNIT) HDRD,ICNTRL
CALL WRTITL(TITLEA,NTITLA,UNIT,-1)
WRITE(UNIT) NSET1,NSET2
WRITE(UNIT) (IND1(I1),I1=1,NSET1)
WRITE(UNIT) (IND2(I2),I2=1,NSET2)
and then nframes of
WRITE(UNIT) ((CO(I1,I2),I1=1,NRES1),I2=1,NRES2)
Where ICNTRL is a 20 element integer array with the following data:
ENDDO
ICNTRL(1) = (STOP - BEGIN)/SKIP
ICNTRL(2) = BEGIN
ICNTRL(3) = SKIP
ICNTRL(4) = STOP - BEGIN
ICNTRL(5) = NSAV
ICNTRL(8) = NDEGF
ICNTRL(9) = NATOM - NFREAT
CALL ASS4(ICNTRL(10),SKIP*DELTA)
IF(LNOE) THEN
ICNTRL(11) = 1
ELSE
ICNTRL(11) = 0
ENDIF
IF(LRESI) THEN
ICNTRL(12) = 1
ELSE
ICNTRL(12) = 0
ENDIF
and NSET1[2] are the number of atoms comprising the two selections and
IND1[2](NSET1[2]). The distance matrix CO(NRES1,NRES2) is a 2-D array of
size either NSET1 x NSET2 or NRES(NSET1) x NRES(NSET2) depending on
whether the residue flag was used in processing the commands
Examples of usage:
------------------
1. Compute the distance matrix for a single coordinate file (resident
in the main coordinate set) and print this matrix to a file linked to
fortran unit 1.
open unit 1 write form name total.dmat
COOR DMAT SINGLE UNIT 1 SELE ALL END SELE ALL END
2. Compute the side chain-side chain center of geometry distance map
from a single coordinate file and print the distanice matrix to unit 1
zeroing all elements of the matrix with distances greater than 6.5
angstroms
define bb select ( type ca .or. type n .or. type c .or. typ o ) end
define side select ( (.not. bb) .and. (.not. hydrogen) ) end
open unit 1 write form name side.dmat
coor dmat residue_average single unit 1 cutoff 6.5 select side end -
select side end
3. Compute the average hydrogen atom-hydrogen atom distance map from
a trajectory file on unit 10 and print the average distance matrix to
unit 1. Use NOE inverse-sixth power weighting in the averaging and
"filter-out" all distances in the final map with values greater than
6.0 angstroms.
open unit 10 read unform name trajectory.crd
open unit 1 write form name noe.dmat
coor dmat unit 1 cutoff 6.0 noe_weighting select hydrogen end -
select hydrogen end -
first_unit 10 nunit 1 begin 100 skip 100 stop 10000
4. Compute the center-of-gemoetry distance matrix for side chains and
write this as a binary "trajectory" file to unit 1. Read the
trajectory from unit 10.
open unit 10 read unform name trajectory.crd
open unit 1 write unform name side.dm-trj
define bb select ( type ca .or. type n .or. type c .or. typ o ) end
define side select ( (.not. bb) .and. (.not. hydrogen) ) end
coor dmat residue_average unit 1 traj select side end select side end -
first_unit 10 nunit 1 begin 100 skip 100 stop 10000
5. Compute the center-of-geometry contact map probability based on a
precomputed distance matrix (e.g. from a PDB structure) based on a 6.5 A
cutoff. (This example is for the interdomain (helix-helix) contacts in
GCN4. The two helices are segids zipa and zipb.)
! First contacts
open unit 1 read unform name "traj/crdp/2zta/2zta_d1-60p.crd"
! trajectory file to use to compute probability from
open unit 2 write form name "distance_matrix/2zta_d1-60p.dmatp"
! file to write contact probability matrix to
open unit 3 read form name "distance_matrix/2zta_full.dmat
! reference contact map
coordinates dmat residue unit 2 -
first 1 nunit 1 begin 100 skip 100 stop 600000 -
select side .and. ( segid zipa ) end -
select side .and. ( segid zipb ) end -
probability uprb 3 tole 0.3 cutoff 6.5
close unit 1
close unit 2
close unit 3
6. The following example shows the use of the dmat command to count the
number of contacts (native and non-native) throughout the course of a
trajectory using the distance matrix projection operator and the fact
that the number of contacts are accessible through the ?ncontact variable.
label dotraj
! Now we loop over the trajectory and compute time dependent properties
open unit 1 read unform name "traj/crdp/2zta/2zta_d1-60p.crd"
open unit 10 write form name "distance_matrix/2zta_d1-60p.traj"
write title unit 10
*# Properties for Contacts
*# trajectory 2zta_d1-60p.
*# time(ps) C(native) C(total)
*
traj iread 1 nread 1 begin 500 skip 500 stop 600000
set time 1.0
set frame 1
label loop
trajectory read
! First get the contact information
open unit 3 read form name "distance_matrix/2zta_full.dmatp"
! reference distance matrix to use for projection
open unit 2 write form name "distance_matrix/temp.dmat"
! junk distance matrix
coor dmat single residue unit 2 cutoff 6.5 -
select ( side .and. segid zipa ) end -
select ( side .and. segid zipb ) end -
proj uprj 3
set cnat ?ncontact
open unit 2 write form name "distance_matrix/temp.dmat"
coor dmat single residue unit 2 cutoff 6.5 -
select ( side .and. segid zipa ) end -
select ( side .and. segid zipb ) end
set ctot ?ncontact
! Write information to file
write title unit 10
* @time @cnat @ctot
incr time by 1.0
incr frame by 1
if frame lt 1200 goto loop
------------------------------------------------------------------------------
19) The ANALysis command
Analysis module for computing solvent averaged properties
It is accessed from the coordinate manipulation
part (CORMAN) of CHARMM and is used with the following syntax. This
piece of documentation is still under development. CLBIII 1/1/1990
NOTE: Keyword syntax changed after c25a2!!
Unit numbers for output to file have to be specified, and
the trajectory is now specified in the usual way with BEGIN,SKIP,STOP
LNI 11/11/96
Keywords:
(SOLVent: specifies analysis is to be of pure solvent, which means xref, yref
and zref, or site keywords are inappropriate, i.e., analysis all configurations
of solvent using all solvent molecules. OBSOLETE)
WATEr: specifies the solvent is water (acutally any three-site molecule),
and forces all distinct g(r)'s to be computed, i.e., g_oo, g_oh and g_hh.
The first atom selection specifies the solvent atoms/molecules to be analyzed.
(SPECies: specifies the solvent species. If SOLVent is active then all
solvent molecules to be analyzed should be specified here, e.g., all of them
present in the simulations. This keyword is followed by the standard selection
syntax and is terminated with the FINIsh_solvent_specification keyword.
OBSOLETE)
SITE: Specifies the collection of atoms around which you would like to compute
solvent properties, e.g., if you would like to analyze the solvent distribution
and velocity correlation function around the center of geometry of a trp
residue this keyword would be followed by the selection syntax which selects
that residue.
XREF, YREF, ZREF: specifies that solvent analysis around a specific spatial
position, (xref, yref, zref) is to be carried out. This is the same as the
site keyword, as far as the analysis of solvent configurations it invokes,
however, this site is static whereas the SITE keyword permits selection of a
dynamically evolving site. The above dimensions ar taken from trajectory stored
informtion for crystal runs (w/ charmm22 or later)
CROSs: allows the selection of two subset of atoms for g(r) analysis
(a&b: 'a' are the atoms specified by the first selection and 'b' are the atoms
specified by the second selection). The g(r) for a-vs-b and b-vs-b are
calculated and returned in units IOH and IHH respectively.
g(r) for a-vs-a will be returned in unit IGDIst.
Note that CROSs does not exclude form the analysis the couple of atoms
belonging to the same segid since it is design for the analysis of
independent subset of solvent molecules.
NOTE:
The keyword CROSs cannot be selected with the following options:
WATer, SITE, IKIRkg, ISDIst, IFDBf.
IVAC, IMSD, IFMIn were not tested with CROSs.
IVAC cannot be combined with any analysis requiring coordinates
IGDIST and ISDIST are mutually exclusive flags
NCORs = number of steps to compute vac or msd
RSPIn = inner radius for vac,msd, analysis around REF (or SITE)
RSPOu = outer radius for vac,msd, analysis around REF (or SITE)
RDSP = radius of dynamics sphere, used for densities, kirkwood and dbf
DENS = density (atoms/A**3) to use in normalization of g(r) if the value
as calculated from the density within RDSP is not satisfactory
DR = grid spacing for analysis of rdf's
RSPHere = radius around REF to use for rdf analysis
MGN = number of points in g(r) curve
RCUT = radius of interaction sphere in dbf calculation
ZP0 = initial reference site - dynamics sphere origin separation
NZP = number of separations to compute dbf
TYP = for DBF calc 1=oxygen, 1=hydrogen
IHIS = unit for output of 3Dhistogram data (in "DN6" format) or
IPDB = unit for output of "atoms" where density exceeds THREshold
with options:
WEIG use WMAIN to weight points !! Not tested
DIPO accumulate dipole vector density !! NOT working yet (June 98)
CHARge accumulate charge density !! Not tested
default is to just accumulated number density of sel. atoms
NORM value densities are divided by this value (and by number of frames)
(default 1)
XMIN,XMAX,DX
YMIN,YMAX,DY grid dimension&spacing (default +/- 20A,0.5A spacing)
ZMIN,ZMAX,DZ
THREshold value for density to output atoms in PDB file format
The atoms indicated by the solvent selection are analyzed. If dipole
data is to be analyzed the selection should contain 1 atom/group - the
groups define what atoms are to be used for the dipole calculation.
This could be automated; also need minimum image combined with orienting
function.
IDIP specifies a unit to which a simple dipole distribution will be plotted.
This facility is intended for use with polarisable modelling of bulk
solvent, and requires the FLUCQ compilation keyword for activation.
(If IDIP is not specified, then no distribution is plotted.)
MINDipole real The minimum dipole (in Debye) to plot (default 0)
MAXDipole real The maximum dipole to plot (default 4.0 Debye)
NUMDipole int The number of sampling points to use (default 100)
EXVC EXcludedVolumeCorrection for use with ISDIST - the soulte-solvent g(r)
is corrected for the volume excluded around the solute (ie the SITE)
by the atoms in the selection following EXCV. This correction is
computed using a Monte Carlo procedure with parameters:
MCP int Total number of points to use in the Monte Carlo
(default 1000)
MCSHells int Total number of equal volume shells to spread
the MCP in (10)
RPRObe real Probe radius (1.5A); a point is considered as excluded
if it is within RPRObe+VDWR(i) of any atom i in
the EXVC set
ISEEd int Seed for random number generator (3141593)
EXAMPLES: (See also the test/c27test/solanal2.inp testcase)
The following examples use a trajectory of a short peptide in a periodic
water box
! MeanSquareDisplacement of all watermolecules to estimate diffusion coeff
open unit 21 read unform name @9pept500.cor
open unit 31 write form name @9pept500.msd
coor anal select type oh2 end - ! what atoms to look at
firstu 21 nunit 1 skip 10 - ! trajectory specification
imsd 31 - ! flag to do the MSD analysis
rspin 0.0 rspout 999.9 - ! we are interested in ALL waters
ncors 20 - ! compute MSD to NCORS*SKIP (0.04ps)steps
xbox @6 ybox @7 zbox @8 ! and we did use PBC
! g(r) for the waters; the program defaults are used to calculate the density
! using selected atoms within 10A (RDSP keyword) of the reference point (0,0,0)
! (REF keyword)
open unit 21 read unform name @9pept500.cor
open unit 31 write form name @9pept500.goo
open unit 32 write form name @9pept500.goh
open unit 33 write form name @9pept500.ghh
! specify WATEr to get all three g(r) functions computed
coor anal water select type OH2 end -
firstu 21 nunit 1 skip 10 - ! trajectory specification
igdist 31 ioh 32 ihh 33 - ! flag to do the solvent-solvent g(r)
mgn 100 dr 0.1 - ! comp. g(r) at MGN points separated by DR
rsph 999.9 - ! use ALL waters for rdf calculation
xbox @6 ybox @7 zbox @8 ! and we did use PBC
! g(r) backbone amide hydrogen - water oxygens
! if a single solute atom is looked at the MULTi keyword is not necessary
! when several solute atoms are specified as the site, their average position
! will be used as the reference position if MULTi is not present
open unit 21 read unform name @9pept500.cor
open unit 31 write form name @9pept500.gonh
coor anal select type oh2 end - ! Water oxygens
site select type H end multi - ! and the amide hydrogens
firstu 21 nunit 1 skip 10 - ! trajectory specification
isdist 31 - ! do the g(r) (here solute-solvent)
mgn 100 dr 0.1 - ! comp. g(r) at MGN points separated by DR
rsph 999.9 - ! we use ALL waters for the calculation
xbox @6 ybox @7 zbox @8 ! and we did use PBC
! g(r) for GLY3 NH - the water oxygens - with excluded volume correction
open unit 21 read unform name @9pept500.cor
open unit 31 write form name @9pept500.gn3ox1
coor anal select type OH2 end -
site multi select atom pept 3 H end -
EXVC select segid pept end -
MCPoints 2000 MCSHells 20 RPRObe 1.7 -
firstu 21 nunit 1 skip 50 - ! trajectory specification
isdist 31 - ! flag to do the solvent-solvent g(r)
mgn 100 dr 0.1 - ! comp. g(r) at MGN points separated by DR
rsph 999.9 - ! we use ALL waters for the calculation
xbox @6 ybox @7 zbox @8 ! and we did use PBC
- Subcommand RCOR (Rotational Correlation Time of Water)
Calculation of rotational correlation times corresponding to the three
rotational motions of a water molecule has been added to the solvent
analysis code. The three rotational motions refer to motion around the
dipole axis (twist), around an axis perpendicular to the molecular
plane (rock) and around an axis parallel to the H-H vector (wag) (Ref 1).
The correlation time is calculated by fitting the exponentional decay part
of the corresponding time correlation function C(t) to an
exponentional function of the form C(t) = A exp(-t/tau) where tau is
the correlation time. The direct correlation functions were calculated
via FFT method using the CORFUNC subroutine in the CORREL.SRC. The
calculation can be invoked by assigning a non-zero integeer value to
the keyword RCOR.
Keywords for rotational correlational time calculation are:
RCOR <integer> - if RCOR > 0, invokes rotational correlational time analysis
ROUT <unit> - write the three correlation functions of selected waters
into a fortran unit
TLOW <real> - lower limit of time for fitting, default is 1.0ps
TUP <real> - upper limit of time for fitting, default is 4.0ps (Ref 2)
MAXT <integer> - maximum number of time steps, default is 512
P1 - compute P1 dipole correlation instead of wag/twist/rock
(< u(t)u(t+tau)>, where u is unit vector along water dipole
output is to unit specified by ROUT
P2 - compute P2 dipole correlation instead of wag/twist/rock
(<P2( u(t)u(t+tau) )>, where u is unit vector along water dipole;
P2(x)=(3x**2-1)/2
output is to unit specified by ROUT
For P1 and P2 the analysis may be performed in a shell defined by RSPIn and RSPOut,
and the minimum image xbox,ybox,zbox is also accounted for
REFERENCE:
1. Johannesson, H. and Halle, B. J. Am. Chem. Soc. 1998, 120, 6859-6870
2. Wallqvist, A. and Berne, B. J. J. Phys. Chem. 1993, 97, 13841-13851
EXAMPLE: see test/c27test/solanal2.inp
! Rotational Correlation Time of Water
open unit 21 read unform name @9pept500.cor
open unit 31 write form name @9pept500.rcor
coor anal sele .byres. (type oh2 - ! select all three atoms of water
.and. (resn asp .and. type od1) -
.around. 3.5) show end -
firstu 21 nunit 1 skip 10 -
rcor 1 - ! rot corr time calculation
timl 1.0 timu 3.0 - ! lower and upper time limits for linear fit
rout 31 - ! corr coef to unit 31
xbox @6 ybox @7 zbox @8 ! and we did use PBC
- Subcommand IHYD: Hydration Number Calculation
This is to calculate hydration number or, in general, the number of solvent
molecules within a specified distance of a multi atom or single atom site:
* number of solvent molecules (residues) withn RHYD of the solute
* number of solvent atoms within RHYD of the solute
* number of solvent atoms within RHYD of solute atoms (ie, if three water
molecules are all within RHYD of a 7-atom solute this will be 63)
Sets CHARMM variables NHYDRR, NHYDAR and NHYDAA to the averages for these
three numbers.
If IHYDN>0 these numbers are written to unit IHYD every timestep.
At the end averages over the trajectory are printed in the output file.
Hydration number calculation is invoked by specifying a non-zero cutoff RHYD.
NB! You need keyword MULTi if the solute (the SITE) has more than one atom.
Keywords for hydration number calculation are:
IHYD <integer> - if IHYDN > 0, output to unit IHYDN each timestep
RHYD <real> - calculate hydration number at this distance from
each atom in the site
Example:
! Calculate hydration no
coor anal sele resn tip3 .and. type oh2 end -
site select resn asp .and. type od1 show end multi -
firstu 21 nunit 1 skip 5 -
rhyd 3.0 - ! calculate hyd no at 3.0A
xbox @6 ybox @7 zbox @8
------------------------------------------------------------------------------
20) The DRAW command
The DRAW command (called directly from CORMAN, not to be
confused with the DRAW command found under the ANALysis command)
is useful for displaying molecules. The output is a command
file that can be read by various displaying and plotting programs.
This command file can be edited for different types of displaying.
In addition to atom positions and bonds, velocity and forces may
also be displayed. The current keywords are:
NOMO - No molecule option (only velocities or derivatives)
DFACt - Derivative factor (default 0.0)
DASH - Spacing of dashed line used for Hbonds (default .01)
FRAMe - Specifies that a frame tag will be written first
(default - dont specify frame)
RETUrn- Specifies which stream the plotting program will
return to after plotting this section (default none)
An atom selection is also looked for. Any atom not selected will
not be considered. The default is to include all atoms.
------------------------------------------------------------------------------
21) The HBONd command
The CONTact command
The HBONd command analyses a trajectory, or the current coordinates,
for hydrogen bonding patterns.
The form COOR CONTact ... ignores the hydrogen bond donor/acceptor
definitions in the psf and looks for all contacts which satisfy the
distance cutoff criterion between all atoms in the two selections; possibly
bridged by a residue as defined by the BRIDge keyword. This is useful for
hydrophobic contact analysis, or for salt bridges. No angle cutoff can
be used with this form of the command.
Output and other options are as for the COOR HBONd variant.
The form COOR HBONd makes use of the DONOR/ACCEPTOR definitions in the psf.
For each acceptor/donor in the first selection the average number and average
lifetime (for trajectories only) of hydrogen bonds to any atom in the second
selection is calculated. A hydrogen bond is assumed to exist when two
candidate atoms are closer than the value specified by CUT (default 2.4A,
(reasonable criterion, DeLoof et al (1992) JACS 114,4028), and if a value
for CUTAngle is given the angle formed by D-H..A is greater than this CUTAngle
(in degrees, 180 is a linear H-bond); the default is to allow all angles.
The current implementation assumes that hbonding hydrogens are present in
the PSF and uses ACCEptor and DONOr information from the PSF to determine
what pairs are possible. If output is wanted to a separate file the IUNIt
option can be used. If the BRIDge option is used the routine calculates average
number and lifetime of bridges formed between all pairs of atoms in the
two selections; a bridge is counted when a residue of the type specified with
the BRIDge <resnam> hydrogen bonds (using same criteria as for direct
hbonding) to at least one atom in each selection. The typical
use of this would be to find water bridges. Here again, results are presented
for each atom in the first selection.
If FIRSTunit is not specified the current (MAIN) coordinates are analyzed.
Keyword VERBose provides a more detailed output:
For trajectory analysis the duration and endtime (ps) of each H-bond,
or bridge, together with a specification of the atoms involved is output;
potentially very large amounts of data! Only hbonds/bridges with a lifetime
longer than the value specified by keyword TCUT (default 0.0 ps) are included
here and in the summary.
NB: TCUT (and NSKIP) may influence the results, since hbonds with
a duration < TCUT are not counted, and for the lifetime analysis a quick
fluctuation in hbond distance may with one choice of NSKIP result in the
hbond being perceived as broken at that instant, whereas with a longer NSKIP
the event would not have been noticed, resulting in a longer lifetime
being reported.
For single coordinate set analysis the VERBose keyword results in a more
detailed listing giving all atoms involved, and also the geometry for
direct hbonds.
For each donor/acceptor in the first selection the trajectory analysis outputs
the AVERAGE NO. of hydrogens bonds this atom has had during the trajectory
(aveno=sum over frames(number of hbonds formed by this atom)/(number of frames)
the average lifetime is defined as
avelife=
sum over hbonding events(duration of hbond between two atoms)/(number of
different hbonds formed by these atoms)
(ie, hbonds that have been broken for at least one frame between events)
Note that the lifetime can be influenced by end-effects (ie hbonds
still active at end of trajctory are counted as being terminated then!)
Output can be directed to a separate file specified by IUNIT int.
The following charmm substitution parameters are set in the module:
?NHBOND = total number of hydrogen bonds for selected atoms (timeaveraged)
?AVNOHB = average number of hydrogen bonds over selected atoms (timeaver.)
?AVHBLF = average lifetime of hydrogen bonds
Note that these averages are over the selected atoms, which may include
a number of atoms with no hbonds > TCUT!
Distance and lifetime histograms can be computed for all (putative) hydrogen
bonds encountered in the analysis; ie, the distance histogram will in general
contain non-zero data also for bins > CUT. For bridges the lifetimes are those
of the bridging events, but the distances are computed from all individual
hydrogen bonds.
The three columns in the output are:
distance (or time) counts counts/NSTEP
where NSTEP is the number of frames that have been analyzed from the
trajectory.
Keyword default meaning
IRHI -1 unit to which distance histogram will be written
DRH 0.05 bin size for distance histogram (A)
RHMAx 10.0 distance in maximum bin (collects all distances >= RHMAx)
ITHI -1 unit to which lifetime histogram will be written
DTH 5.0 bin size for lifetime histogram (ps)
THMAx 1000.0 time in maximum bin (collects all times >= THMAx)
NOTE: In order not to find hbonds between bonded atoms UPDATE is called,
which requires coordinates to be present when invoking this module. Since
this is done just to get the non-bond exclusion lists, the cut-offs are
set to very small values, and could influence subsequent energy evaluations
if the non-bond cutoffs are not then respecified.
------------------------------------------------------------------------------
22) The HISTogram command
This command computes a histogram along the X,Y,Z or Radial directions
for the selected atoms.
The histogram can either be a simple count of the number of atoms
contained in each bin (specified by the HNUM=number of bins between
HMIN,HMAX keywords), or if the WEIGhting keyword is present the WMAIN
array is summed for the atoms in each bin.
HSAVe specifies that the histogram should be saved and incremented at
the next invocation of COOR HIST. HPRInt specifies that the resulting
histogram should be printed. For X,Y,Z histograms the output is
the accumulated density/HNORM (default=1.0) in each bin. If HDENS>0.0
(default=0.0) there is also a third column for R histograms containing
the accumulated density/(volume of shell containing this bin)/DENS.
The COMParison keyword results in XCOMP,YCOMP,ZCOMP,WCOMP being used.
The variable ?NCONFIG is set to the number of configurations (frames)
that have been accumulated so far.
The results may be output to a file specified by IUNIt int.
EXAMPLE:
To average the charge density in spherical shells from a trajectory
could be done in the following way:
scalar wmain=charge
traj iread ....
set i 1
label loop
traj read
!if you are reading velocities, you may want to convert to A/ps
! (and then you wouldn't use the weighting option like this)
! scalar x divi ?TIMFAC
! scalar y divi ?TIMFAC
! scalar z divi ?TIMFAC
coor hist R hnum 50 hmin 0.0 hmax 10.0 hsave weig
incre i by 1
if i .lt. 100 goto loop
! you could also normalize for number of selected atoms
! set scale ?NSEL
! mult scale by ?NCONFIG
! then use @scale instead of ?NCONFIG below
bomblevel -1 ! to get by the zero atom selected warning below
coor hist R hnum 50 hmin 0.0 hmax 10.0 select none end hprint -
hnorm ?NCONFIG [ hdens 0.03 (some reasonable bulk density/A**3) ]
------------------------------------------------------------------------------
23) The PUCKer command
COORdinates PUCKer [SEGId segid] RESId resid1 [TO resid2] [AS | CP]
The sugar pucker phase and amplitude, as defined by
Altona&Sundaralingam (default, keyword AS) or (CP) Cremer&Pople (JACS 1975),
are calculated for the (deoxy)ribose of the specified residue(s);
the first segment is the default. A range of residues from resid1 TO resid2
can be analyzed.
------------------------------------------------------------------------------
24) The INERtia command
COORdinates INERtia [atom-selection]
Principal moments of inertia I_xx, I_yy, I_zz are calculated and
the eigenvectors of the inertia tensor are printed. Normally atom selection
should not be used and the command
example:
COOR INER
is sufficient, since all ithe atoms are selected by default. The units for
principal moments of inertia are
amu * A^2, where amu - atomic mass unit (Carbon is 12), and A stands
for Angstrom.
------------------------------------------------------------------------------
25) The INERtia ENTRopy command
COORdinates INERtia [atom-selection] ENTRopy
[TEMPerature <real>] [SIGMa <real>]
Entropy calculation is an extention to the INERtia command.
In addition to calculation of principal moments of inertia the rotational
and translational entropy components will be evaluated. Calculation of
these two entropy terms is very fast. See vibran.doc to see how to
calculate the vibrational entropy term.
Default value for TEMPerature is 298.15 K. Default SIGMa value is 1.0.
SIGMa is symmetry number which is 1 for non-symmetric molecule and some
low symmetry groups. For symmetric molecules one should enter a correct
value for sigma (see, for example, C.J.Cramer, "Essentials of Comp.Chem.",
2002,p.327).
example:
COOR INER ENTRopy
The units for entropy are cal/(mol*K). Rotational and translational
entropy terms can be accessed in CHARMM input file as ?SROT and ?STRA
substitution parameters.
Coordinate Manipulation Values
There are several different variables that can be used in titles or
CHARMM commands that are set by some of the coordinate manipulation commands.
Here is a summary and description of each variable.
----------------------------------------------------------------------------
'XAXI','YAXI','ZAXI','RAXI','XCEN','YCEN','ZCEN'
A rotation axis vector and its length and the center of rotation.
This data is set by the COOR AXIS, COOR LSQP, COOR ORIE, and COOR ORIE RMS
commands. These values may be used by any of the commands that uses the
vector-spec with the AXIS keyword.
----------------------------------------------------------------------------
'XMIN','YMIN','ZMIN','WMIN','XMAX','YMAX',
'ZMAX','WMAX','XAVE','YAVE','ZAVE','WAVE'
Statistics set by the COOR STAT command.
----------------------------------------------------------------------------
'THET'
Angle of rotation set by the COOR ORIEnt command.
----------------------------------------------------------------------------
'XMOV','YMOV','ZMOV'
Displacement of centers set by the COOR ORIEnt command.
----------------------------------------------------------------------------
'RMS'
Resulting RMS value set by the COOR RMS, COOR ORIEnt, or COOR RGYR
commands.
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute