D. Residue Topology Files

Table 47. Amino acid residue topology files (AMINO.RTF and AMINOH.RTF) 

Name	Type	Description
ABU	Residue	Gamma amino butyric acid
ACE	Residue	Adds acetamide group to N-terminus
ALA	Residue	L-alanine
ANAP	Residue	Alpha naphthyl alpha phenylalanine
ARG	Residue	L-arginine (charged)
ARGN	Residue	L-arginine (neutral)
ASN	Residue	L-asparagine
ASP	Residue	L-aspartic acid
ASPH	Residue	L-aspartic acid (protonated)
ATP	Residue	Adenosine triphosphate
BAA	Residue	Beta alanine (3-amino propionic acid)
BEN	Residue	Benzamidine inhibitor
BNAP	Residue	Beta naphthyl alpha phenylalanine (polar H only)
CHXA	Residue	Cyclohexylalanine
CIT	Residue	Citrulline
CYS	Residue	L-cysteine
DAA	Residue	Delta amino pentanoic acid (5-amino pentanoic acid)
DPRO	Residue	D-proline
EAA	Residue	6-amino hexanoic acid
FMN	Residue	Flavin mononucleotide
GAA	Residue	Gamma amino butyric acid (4-amino butyric acid)
GDP	Residue	Guanosine diphosphate
GGLU	Residue	Gamma glutamic acid
GLA	Residue	Gamma carboxy glutamic acid
GLN	Residue	L-glutamine
GLU	Residue	L-glutamic acid
GLUH	Residue	L-glutamic acid (protonated)
GLY	Residue	Glycine (uses patch residue GLYP as its default N-terminal patch in AMINO.RTF)
HCYS	Residue	Homocysteine
HIS	Residue	L-histidine (uncharged with a proton on ND1)
HLYS	Residue	Hydroxylysine
HPHE	Residue	Homophenylalanine
HPRO	Residue	Hydroxyproline
HSC	Residue	L-histidine (protonated)
HSD	Residue	L-histidine (uncharged with a proton on NE2; an isomer of HIS)
HSER	Residue	Homoserine
ILE	Residue	L-isoleucine
LEU	Residue	L-leucine
LYS	Residue	L-lysine (charged)
LYSN	Residue	L-lysine (neutral)
MET	Residue	L-methionine
MP3	Residue	3-phosphoglycerate
MPD	Residue	2-methyl-2,4-pentanediol
MTX	Residue	Methotrexate
ORN	Residue	Ornithine
PC	Residue	Phosphocholine, deprotonated re 2mcp of PDB
PCA	Residue
PCLP	Residue	Para chlorophenylalanine
PEN	Residue	Penicillamine
PFP	Residue	Para fluorophenylalanine
PGLY	Residue	Phenylglycine
PHE	Residue	L-phenylalanine
PRO	Residue	L-proline (uses patch residue PROP as its default N-terminal patch)
PSER	Residue	Phosphoserine
PTYR	Residue	Phosphotyrosine
SER	Residue	L-serine
STAO	Residue	Statone
STAI	Residue	Statine
STYR	Residue	Sulfurated tyrosine
THR	Residue	L-threonine
TRP	Residue	L-tryptophan
TYR	Residue	L-tyrosine
UALA	Residue	Dehydroalanine
UPHE	Residue	Z-dehydrophenylalanine
VAL	Residue	L-valine
ZAA	Residue	7-amino heptanoic acid
OH2	Residue	TIPS3P water model (with no bond between the hydrogens)
TIP3	Residue	TIPS3P water model (including bond between the hydrogens for SHAKE)
HOH	Residue	Identical to TIP3
DOD	Residue	Identical to TIP3 (treats D2O as H2O)
ST2	Residue	ST2 water model (including two lone pairs on the oxygen)
WAT	Residue	TIP3P Water model for PDB systole waters
ACCP	Patch residue	Default N-terminal patch for ACC
CALD	Patch residue	Replaces the C-terminus with an aldehyde group
CALC	Patch residue	Reduces the C-terminus carboxyl group to an alcohol
CAMD	Patch residue	Converts the C-terminus to an amide
CAME	Patch residue	Adds a methyl group to the alpha carbon; may not be used with Gly
CBZS	Patch residue	Replaces the C-terminus with a benzyl ester group
CEOH	Patch residue	Converts the C-terminus to an amide of ethanol amine
CETS	Patch residue	Replaces the C-terminus with an ethyl ester group
CGLY	Patch residue	Provides a charged COO- group to Gly at the C-terminus
CH2	Patch residue	Replaces the carbonyl group with CH2
CIS	Patch residue	Converts trans peptides to cis
CMAM	Patch residue	Converts the C-terminus to an N-methyl amide
CMES	Patch residue	Replaces the C-terminus with a methyl ester group
COOH	Patch residue	Adds a proton to the default C-terminal patch
CPHS	Patch residue	Replaces the C-terminus with a phenyl ester group
CTBS	Patch residue	Replaces the C-terminus with a tert-butyl group
CTER	Patch residue	Default C-terminal patch for all standard residues
CTRA	Patch residue	C-terminal patch for all standard residues; may only be applied after the PSF has been generated
CTRU	Patch residue	Provides a charged COO- group to unsaturated amino acids
DCOH	Patch residue	Removes COOH from C-terminus
DEAM	Patch residue	Removes NH3 from N-terminus; should not be used in the Sequence Builder
DISU	Patch residue	Constructs a disulfide bond between two Cys residues
DLNK	Patch residue	Joins the carboxyl group of Asp with the N-terminus to form a cyclic peptide (AMINOH.RTF only)
GLYP	Patch residue	Default N-terminal patch for Gly (AMINO.RTF only)
HPRP	Patch residue	Default N-terminal patch for HPro
ILNK	Patch residue	Joins two segments to form a peptide bond
KLNK	Patch residue	Joins the amino group of Lys with the C-terminus to form a cyclic peptide
LINK	Patch residue	Joins two segments to form a peptide bond; links N to C
LIMG	Patch residue	Same as LNK2 but used to patch IMAGES. In AMINOH.RFT only
LNK2	Patch residue	Same as LINK but links C to N
LNP1	Patch residue	Link patch for proline on the N-terminus (links N to C)
LNP2	Patch residue	Same as above (applied C to N)
LTOD	Patch residue	Converts an L-amino acid to a D-amino acid; may not be used on Pro
NACP	Patch residue	N-terminal acetamide for Pro or HPro
NACT	Patch residue	Replaces the N-terminus with an acetamide group; may not be used with Gly (AMINO.RTF), Pro, or HPro as the first residue (see NACP)
NBOC	Patch residue	Replaces the N-terminus with a tertbutoxylcarbonyl group; may not be used with Gly (AMINO.rtf), Pro, or HPro as the first residue
NCBZ	Patch residue	Replaces the N-terminus with a carbobenzoxyl group; may not be used with Gly (AMINO.rtf), Pro, or HPro as the first residue
NDME	Patch residue	Adds a N,N-dimethyl group to the N-terminus
NETC	Patch residue	Replaces the N-terminus with an ethylcarbonyl group; may not be used with Gly (AMINO.rtf), Pro, or HPro as the first residue
NFA	Patch residue	Replaces N-terminus with C13H27 fatty acid amide
NFAG	Patch residue	Same as NFA but for glycine as the N-terminus
NFRM	Patch residue	Replaces the N-terminus with a formamide group; may not be used with Gly (AMINO.RTF), Pro, or HPro as the first residue
NGUA	Patch residue	Adds a guandino group to the N-terminus; may not be used for Pro
NH2	Patch residue	Deprotonates the charged N-terminus
NMEC	Patch residue	Replaces the N-terminus with a methylcarbonyl group; may not be used with Gly (AMINO.rtf), Pro, or HPro as the first residue
NPHC	Patch residue	Replaces the N-terminus with a phenylcarbonyl group; may not be used with Gly (AMINO.rtf), Pro, or HPro as the first residue
NPME	Patch residue	Replaces the peptide nitrogen hydrogen with a methyl group; may not be applied to the first residue
NPOH	Patch residue	Replaces the peptide nitrogen hydrogen with a hydroxyl group; may not be used on an end residue
NPYG	Patch residue	Converts an N-terminal glutamic acid to pyroglutamic acid
NTER	Patch residue	Default N-terminal patch for all standard residues except Gly and Pro (AMINO.rtf)
NTME	Patch residue	Adds a N-methyl group to the N-terminus
NTOO	Patch residue	Replaces the peptide nitrogen with an ester oxygen; may not be applied with Gly as the ester residue; may only be used on non-terminal residues
NTRA	Patch residue	N-terminal patch for all standard residues except Gly (AMINO.rtf) and Pro; may only be applied after the PSF has been generated
NTRU	Patch residue	Default N-terminal patch for UALA and UPHE
N3ME	Patch residue	Adds a N,N,N trimethyl group to the N-terminus
PROP	Patch residue	Default N-terminal patch for Pro
SING	Patch residue	Used to chanrge the Ca of a single residue after the NTER and CTER patches are applied
ZTOE	Patch residue	Converts Z-dehydrophenylalanine to E-dehydrophenylalanine

Table 48. Nucleic acid residue topology files (DNA.RTF, DNAH.RTF, RNA.RTF, RNAH.RTF) 

Name	Type	Description
G	Residue	Deoxyguanosine (DNA.RTF and DNAH.RTF)
G	Residue	Guanosine (RNA.RTF and RNAH.RTF)
A	Residue	Deoxyadenosine (DNA.RTF and DNAH.RTF)
A	Residue	Adenosine (RNA.RTF and RNAH.RTF)
C	Residue	Deoxycytidine (DNA.RTF and DNAH.RTF)
C	Residue	Cytidine (RNA.RTF and RNAH.RTF)
T	Residue	Deoxythymidine (DNA.RTF and DNAH.RTF)
T	Residue	Thymidine (RNA.RTF and RNAH.RTF)
U	Residue	Uridine (RNA.RTF and RNAH.RTF)
CAMP	Residue	Cyclic AMP (RNA.RTF and RNAH.RTF)
2END	Patch residue	Modifies ribose to a 2' endo conformation
DEOX	Patch residue	Converts ribose to deoxyribose
FC	Patch residue	Fully charges the phosphate group
5PHO	Patch residue	Places a phosphate group at the 5' end
3PRI	Patch residue	Places an OH at the 3' end after PSF generation
5PRI	Patch residue	Places a phosphate at the 5' end after PSF generation
PUR	Patch residue	Patch for purine bases similar to PYR
PYR	Patch residue	Patch to add H1 to pyrimidines when using base only
5TER	Patch residue	Places a hydroxyl group at the 5' end
3TER	Patch residue	Places a hydroxyl group at the 3' end

Table 49. Carbohydrate residue topology file (POLYSACCHARIDEH.RTF) 

Name	Type	Description
FRUC	Residue	beta D fructose
FUC	Residue	beta L fucose
GAL	Residue	beta D galactose
GCU	Residue	beta D glucuronic acid
GLU	Residue	beta D glucose
GLUC	Residue	beta D glucose
MAN	Residue	beta D mannose
NAG	Residue	beta D N-acetyl glucosamine
NAM	Residue	beta D N-acetylmuramic acid
RIBO	Residue	beta D ribose
SIQ1	Residue	alpha D-sialic acid (Brady+CHARMm charges)
SIA2	Residue	alpha D-sialic acid (CINDO charges)
AL11	Patch residue	Constructs an aldose link 1-1 (alpha)
AL12	Patch residue	Constructs an aldose link 1-2 (alpha)
AL13	Patch residue	Constructs an aldose link 1-3 (alpha)
AL14	Patch residue	Constructs an aldose link 1-4 (alpha)
AL16	Patch residue	Constructs an aldose link 1-6 (alpha)
ALLO	Patch residue	Converts glucose to allose
ALPH	Patch residue	Converts beta-pyranoses to alpha-pyranoses
ALTR	Patch residue	Converts glucose to altrose
36AN	Patch residue	Creates a 3-6 anhydro galactose
1ASN	Patch residue	Links a pyranose to asparagine ND2
BE11	Patch residue	Constructs an aldose link 1-1 (beta)
BE12	Patch residue	Constructs an aldose link 1-2 (beta)
BE13	Patch residue	Constructs an aldose link 1-3 (beta)
BE14	Patch residue	Constructs an aldose link 1-4(beta)
BE16	Patch residue	Constructs an aldose link 1-6 (beta)
COH	Patch residue	Generates uronic acids from an aldose
GALA	Patch residue	Converts glucose to galactose
GULO	Patch residue	Converts glucose to gulose
IDO	Patch residue	Converts glucose to idose
LHEX	Patch residue	Converts D-pyranoses to L-pyranoses
MANN	Patch residue	Converts glucose to mannose
NAG2	Patch residue	Adds an N-acetyl group at the 2-carbon
2NH3	Patch residue	Converts glucose to glucoseamine (2-carbon)
OME	Patch residue	Joins beta O_ME group at C1
2PO4	Patch residue	Constructs a phosphate ester to the hydroxyl group at the 2-carbon
3PO4	Patch residue	Constructs a phosphate ester to the hydroxyl group at the 3-carbon
4PO4	Patch residue	Constructs a phosphate ester to the hydroxyl group at the 4-carbon
6PO4	Patch residue	Constructs a phosphate ester to the hydroxyl group at the 6-carbon
PROT	Patch residue	Links a pyranose to a serine hydroxyl group
SA23	Patch residue	Joins O2 of sialic acid to O3 of Gal
SER	Patch residue	Links a pyranose to a serine hydroxyl group; uses Brady-CHARMm charges
SG23	Patch residue	Links a pyranose to a serine hydroxyl group; uses CINDO charges
2SO4	Patch residue	Constructs a sulfate ester to the hydroxyl group at the 2-carbon
3SO4	Patch residue	Constructs a sulfate ester to the hydroxyl group at the 3-carbon
4SO4	Patch residue	Constructs a sulfate ester to the hydroxyl group at the 4-carbon
6SO4	Patch residue	Constructs a sulfate ester to the hydroxyl group at the 6-carbon
TALO	Patch residue	Converts glucose to talose
1THR	Patch residue	Links a pyranose to Thr hydroxyl
1TYR	Patch residue	Links a pyranose to Tyr hydroxyl
XYLO	Patch residue	Converts D-glucose to D-xylose

Table 50. Assorted metal ions topology file (IONS.RTF) 

Name	Type	Description
AG	Residue	Silver ion
AL	Residue	Aluminum ion
AU	Residue	Gold ion
BA	Residue	Barium ion
BE	Residue	Beryllium ion
BR	Residue	Bromine ion
CA	Residue	Calcium ion
CD	Residue	Cadmium ion
CL	Residue	Chlorine ion
CO	Residue	Cobalt
CS	Residue	Cesium ion
CU	Residue	Copper ion +1
F	Residue	Fluorine ion
FE	Residue	Iron +2
GA	Residue	Gallium
HG	Residue	Mercury
I	Residue	Iodine
IN	Residue	Indium
K	Residue	Potassium ion
LI	Residue	Lithium ion
MG	Residue	Magnesium ion
MN	Residue	Manganese +2
MO	Residue	Molybdenum
NA	Residue	Sodium ion
NI	Residue	Nickel
PB	Residue	Lead +2
PD	Residue	Palladium
PO4	Residue	Phosphate group
PT	Residue	Platinum
RB	Residue	Rubidium
SN	Residue	Tin
SO4	Residue	Sulfate group
SR	Residue	Strontium
TI	Residue	Titanium
V	Residue	Vanadium
ZN	Residue	Zinc ion
ZR	Residue	Zirconium

Table 51. Porphyrin topology file (PORPHYRINH.RTF) 

Name	Type	Description
BCL	Residue	Bacteriochlorophyll a (minus the Mg)
BCMG	Residue	Bacteriochlorophyll with Mg2+
CHPA	Residue	Chlorophyll a with phytyl sidechain
CHPB	Residue	Chlorophyll b with phytyl sidechain
CO	Residue	Carbon monoxide
HEM	Residue	Protoporphryn IX
HEMO	Residue	Porphryn IX with Fe and O2 with no Fe-O bonds
O2	Residue	Diatomic oxygen
PCL	Residue	Phytochlorophyll without Mg2+
PPX	Residue	Protoporphryn IX with no Fe
PRIX	Residue	Protoprophyrin IX
PFE	Patch residue	Adds Fe to protoporphryn IX to make heme
PLO2	Patch residue	Attaches O2 and HIS to HEM
PLIG	Patch residue	Attaches CO and HIS to HEM
PMG	Patch residue	Adds Mg to bacteriochlorophyll

Table 52. Protein Data Bank topology file (PDBAMINO.RFT) 

Name	Type	Description
ABU	Residue	Gamma amino butyric acid
ACE	Residue	Adds acetamide group to N-terminus
ALA	Residue	Alanine
ALB	Residue	Beta alanine
ARG	Residue	Arginine
ARGN	Residue	Neutral arginine
ASN	Residue	Asparagine
ASP	Residue	Aspartic acid
ASPH	Residue	Protonated aspartic acid
ATP	Residue	Adenosine triphosphate
BEN	Residue	Benzamidine inhibitor
CYS	Residue	Cysteine
FMN	Residue	Flavin mononucleotide
GDP	Residue	Guanosine diphosphate
GLN	Residue	Glutamine
GLU	Residue	Glutamic acid
GLUH	Residue	Protonated glutamic acid
GLY	Residue	Glycine
HIS	Residue	Histidine (uncharged, proton on ND1)
HSC	Residue	Protonated histidine
HSD	Residue	Histidine isomer (proton on NE2)
HSE	Residue	Homoserine
HYL	Residue	Hydroxyproline
ILE	Residue	Isoleucine
LEU	Residue	Leucine
LYS	Residue	Lysine
LYSN	Residue	Neutral lysine
MET	Residue	Methionine
MP3	Residue	3-phosphogycerate
MPD	Residue	2-methyl-s, 4-petanediol
MTX	Residue	Methotrexate
ORN	Residue	Ornithine
PC	Residue	Phosphocholine, deprotonated
PCA	Residue
PEN	Residue	Penicillamine
PHE	Residue	Phenylalanine
PRO	Residue	Proline
SER	Residue	Serine
ST2	Residue
THR	Residue	Threonine
TRP	Residue	Tryptophan
TYR	Residue	Tyrosine
VAL	Residue	Valine
HOH	Residue	TIP3P water model for PDB crystal waters
OH2	Residue	Water
TIP3	Residue	Water model
WAT	Residue	TIP3P water model for crystal waters
ACCP	Patch residue	N-terminal patch for ACC.
CALC	Patch residue	Reduces C-terminal carboxyl to an alcohol
CALD	Patch residue	Replaces C-terminus with an aldehyde group (Apply this patch only after the CTER patch has been applied.)
CAMD	Patch residue	Converts the C-terminus to an amide
CAME	Patch residue	Alpha methyl patch for all residues except glycine
CBZS	Patch residue	Replaces C-terminus with a benzyl ester group (Apply this patch only after the CTER patch has been applied.)
CETS	Patch residue	Replaces the C-terminus with a ethyl ester group (Apply this patch only after the CTER patch has been applied.)
CGYL	Patch residue	Provides a charged COO- group to Gly C-terminal
CH2	Patch residue	Replaces the carbonyl group in the backbone by CH2
CIS	Patch residue	Converts trans peptide to cis
CMAM	Patch residue	Converts the C-terminus to an N methyl-amide
CMES	Patch residue	Replaces the C-terminus with a methyl ester group (Apply this patch only after the CTER patch has been applied.)
COOH	Patch residue	Protonated carboxyl C-terminus
CPHS	Patch residue	Replaces the C-terminus with a phenyl group (Apply this patch only after the CTER patch has been applied.)
CTBS	Patch residue	Replaces the C-terminus with a t-bytyl ester group (Apply this patch only after the CTER patch has been applied.)
CTER	Patch residue	Provides a charged COO- group for the C-terminus
CTRA	Patch residue	Provides a charged COO- group for the C-terminus
DCOH	Patch residue	Removes COOH from the C-terminus (Not recommended for Pro or Gly.)
DEAM	Patch residue	Removes NH3 from the N-terminus (Doesn't work in Sequence Builder.)
DISU	Patch residue	Patch for disulfides (Requires two Cys.)
DLNK	Patch residue	Connects the carboxyl group of Asp with the N-terminus of a peptide to form a cyclic peptide (Apply this patch as RES (Asp) - RES (N-term).)
GLYP	Patch residue	N-terminal patch for glycine
HPRP	Patch residue	N-terminal patch for Hyp
ILNK	Patch residue
KLNK	Patch residue	Connects the amino group of Lys with the C-terminus (Apply this patch as RES (Lys) - RES (N-term).)
LIMG	Patch residue	Creates a peptide bond between the C-terminus of the primary segment and the N-terminus of its image
LINK	Patch residue	Joins two segments and forms a peptide bond or can be used to form a cyclic peptide (Apply this patch as RES(N-term) - RES (C-term). Do not apply the patch to Gly residues or any residue without an alpha-carbon atom type CH1E.)
LNK2	Patch residue	Joins two segments and forms a peptide bond or can be used to form a cyclic peptide. (Reverse version of LINK) (Apply this patch as RES(N-term) - RES (C-term). Do not apply the patch to Gly residues or any residue without an alpha-carbon atom type CH1E.)
LNP1	Patch residue	Same as LINK except Pro at the N-terminus
LNP2	Patch residue	Same as LNK2 except Pro at the N-terminus
LNPT	Patch residue	Creates a peptide bond between the C-terminus of the primary segment and the N-terminus of its image
LTOD	Patch residue	Converts an L-residue to a D-residue
NACP	Patch residue	Replaces the N-terminal group with a acetamide group
NACT	Patch residue	Replaces the N-terminal group with a acetamide group (This patch does not work with Pro or Gly as the first residue. Apply this patch only after the NTER patch PROP has been applied.)
NBOC	Patch residue	Replaces the N-terminal group with a tert-bul ester group; provides a charged NH3+ group for the N-terminus
NCBZ	Patch residue	Replaces the N-terminus with a carbobenzoxly group (This patch does not work with Pro or Gly as the first residue. Apply this patch only after the NTER patch PROP has been applied.)
NDME	Patch residue	N,N -dimethyl terminal group
NETC	Patch residue	Replaces the N-terminus with an ethyl ester (This patch does not work with Pro or Gly as the first residue. Apply this patch only after the NTER patch PROP has been applied.)
NFA	Patch residue	Replaces the N-terminus with a fatty acid amide C13H27 (This patch does not work with Pro or Gly as the first residue. Apply this patch only after the NTER patch PROP has been applied.)
NFAG	Patch residue	Replaces the N-terminus with a fatty acid amide C13H27 (This patch is specific for Gly at the N-terminus. Apply this patch only after the NTER patch has been applied.)
NFRM	Patch residue	Replaces the N-terminus with a formamide group
NGUA	Patch residue	Replaces the N-terminus with a guanidino group (Do not use for Pro. Change atom type for Ca for Gly and edit dihedrals.)
NH2	Patch residue	Deprotonated N-terminus
NMEC	Patch residue	Replaces the N-terminus with a methylester (This patch does not work with Pro or Gly as the first residue. Apply this patch only after the NTER patch PROP has been applied. Change atom type for Ca for Gly.)
NPHC	Patch residue	Replaces the N-terminus with a phenylester group (This patch does not work with Pro or Gly as the first residue. Apply patch only after the NTER patch has been applied.)
NPME	Patch residue	N-methyl (for peptides) (Not to be applied to first residue.)
NPYG	Patch residue	Converts N-terminal glutamic acid to pyroglutamic acid
NTER	Patch residue	Provides a charged NH3+ group for the N-terminus (This patch does not work with Gly or Pro as the first residue. Use GLYP or PROP. This patch does not work with dehydro amino acids as the first residue.)
N3ME	Patch residue	N,N,N-trimethyl terminal group
NTME	Patch residue	N-methyl amino terminal group
NTOO	Patch residue	Replaces the peptide nitrogen in a residue with an ester oxygen (This patch requires a sequence of three residues where the second residue is the ester residue.)
NTRA	Patch residue	Provides a charged NH3+ group for the N-terminus with angle definitions (This patch does not work with Pro or Gly or with dehydro amino acids as the first residue.)
NTRU	Patch residue	Provides a charged NH3+ group for the N-terminus.
PROP	Patch residue	N-terminal patch for Pro
ZTOE	Patch residue	Converts Z-dehydroPhe to E-dehydroPhe