gromacs-data 4.5.5-2 / usr / share / gromacs / top / gmx.ff / aminoacids.vsd

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/usr/share/gromacs/top/gmx.ff/aminoacids.vsd is in gromacs-data 4.5.5-2.

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The actual contents of the file can be viewed below. 

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; no CH3 groups - ffgmx is a united atom forcefield
[ NH3 ]
   NL        C    MNH3
   NL       CB    MNH3
   NL      CHE    MNH3
   NL      CH1    MNH3
   NL      CH2    MNH3
[ NH2 ]
   NT      planar
   NZ      planar
   NL        C    MNH3
   NL       CB    MNH3
   NL      CHE    MNH3
   NL      CH1    MNH3
   NL      CH2    MNH3

; Data for generating dummy aromatic rings.
; Actually we dont need all these bonds and angles,
; but by specifying them here it is easier to improve
; the dummy generation code later.
[ PHE ]
  CG	CD1		0.139	
  CG	CD2		0.139
  CD1   CE1		0.139
  CD2	CE2		0.139
  CE1   CZ		0.139
  CE2	CZ		0.139
  CD1	HD1		0.108
  CD2	HD2		0.108
  CE1	HE1		0.108
  CE2   HE2		0.108
  CZ    HZ		0.108
  CG    CD1   CE1	120.0
  CD1   CE1   CZ	120.0
  CE1   CZ    CE2	120.0
  CZ    CE2   CD2	120.0
  CE2   CD2   CG	120.0
  CD2   CG    CD1	120.0
  CG    CD1   HD1	120.0
  CG    CD2   HD2	120.0
  HD1   CD1   CE1	120.0
  CD1   CE1   HE1	120.0
  HE1   CE1   CZ	120.0
  CE1   CZ    HZ	120.0
  HZ    CZ    CE2	120.0
  CZ    CE2   HE2	120.0
  HE2   CE2   CD2	120.0
  HD2   CD2   CG	120.0

[ TYR ]
  CG	CD1		0.139	
  CG	CD2		0.139	
  CD1   CE1		0.139	
  CD2	CE2		0.139	
  CE1   CZ		0.139	
  CE2	CZ		0.139	
  CD1	HD1		0.108
  CD2	HD2		0.108
  CE1	HE1		0.108
  CE2   HE2		0.108
  CZ    OH		0.136
  OH    HH		0.100
  CG    CD1   CE1	120.0
  CD1   CE1   CZ	120.0
  CE1   CZ    CE2	120.0
  CZ    CE2   CD2	120.0
  CE2   CD2   CG	120.0
  CD2   CG    CD1	120.0
  CG    CD1   HD1	120.0
  CG    CD2   HD2	120.0
  HD1   CD1   CE1	120.0
  CD1   CE1   HE1	120.0
  HE1   CE1   CZ	120.0
  CE1   CZ    OH	120.0
  CZ    OH    HH	109.5
  OH    CZ    CE2	120.0
  CZ    CE2   HE2	120.0
  HE2   CE2   CD2	120.0
  HD2   CD2   CG	120.0

[ TRP ]
  CB    CG              0.153
  CG	CD1   		0.139
  CD1   NE1		0.133
  NE1	CE2		0.133
  CE2   CD2		0.139
  CD2   CG		0.139
  CE2   CZ2		0.139
  CZ2   CH2		0.139
  CH2   CZ3		0.139
  CZ3   CE3		0.139
  CE3   CD2		0.139
  CD1   HD1		0.108
  NE1   HE1		0.100
  CE3   HE3		0.108
  CZ2   HZ2		0.108
  CZ3   HZ3		0.108
  CH2   HH2		0.108
  CB    CG    CD1       126.0
  CB    CG    CD2       126.0
  CG    CD1   NE1	108.0
  CD1   NE1   CE2	108.0
  NE1   CE2   CD2	108.0
  CE2   CD2   CG	108.0
  CD2   CG    CD1	108.0
  NE1   CE2   CZ2	132.0
  CE2   CZ2   CH2	120.0
  CZ2   CH2   CZ3	120.0
  CH2   CZ3   CE3	120.0
  CZ3   CE3   CD2	120.0
  CE3   CD2   CG	132.0
  CE2   CD2   CE3       120.0
  CD2   CE2   CZ2       120.0
  CG    CD1   HD1	126.0	
  HD1   CD1   NE1	126.0
  CD1   NE1   HE1	126.0
  HE1   NE1   CE2	126.0
  CZ3   CE3   HE3	120.0
  HE3   CE3   CD2 	120.0
  CE2   CZ2   HZ2	120.0
  HZ2   CZ2   CH2	120.0
  CH2   CZ3   HZ3	120.0
  HZ3   CZ3   CE3	120.0
  CZ2   CH2   HH2	120.0
  HH2   CH2   CZ3	120.0

[ HISA ]
  CG    ND1		0.133
  ND1   CE1		0.133
  CE1   NE2		0.133
  NE2	CD2		0.133
  CD2   CG		0.133
  ND1   HD1		0.100
  CG    ND1   CE1	108.0		
  ND1   CE1   NE2	108.0	
  CE1   NE2   CD2	108.0	
  NE2   CD2   CG	108.0	
  CD2   CG    ND1	108.0	
  CG    ND1   HD1	126.0
  HD1   ND1   CE1  	126.0

[ HISB ]
  CG    ND1		0.133
  ND1   CE1		0.133
  CE1   NE2		0.133
  NE2	CD2		0.133
  CD2   CG 		0.133
  NE2   HE2		0.100	
  CG    ND1   CE1	108.0
  ND1   CE1   NE2 	108.0
  CE1   NE2   CD2	108.0
  NE2   CD2   CG	108.0
  CD2   CG    ND1	108.0
  CE1   NE2   HE2	126.0
  HE2   NE2   CD2	126.0
  
[ HISH ]
  CG    ND1		0.133
  ND1   CE1		0.133
  CE1   NE2		0.133
  NE2	CD2		0.133
  CD2   CG		0.133
  ND1   HD1		0.100
  NE2   HE2		0.100
  CG    ND1   CE1	108.0	
  ND1   CE1   NE2	108.0	
  CE1   NE2   CD2	108.0	
  NE2   CD2   CG	108.0	
  CD2   CG    ND1	108.0	
  CG    ND1   HD1	126.0
  HD1   ND1   CE1	126.0
  CE1   NE2   HE2	126.0
  HE2   NE2   CD2 	126.0

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