Acetylated lysine and negatively charged cysteine for CHARMM protein force-field
The CHARMM protein force-fields in gromacs provides topologies for many commonly found protein residues. However, when one wants to include a slightly more exotic residue - say a modified amino acid - the process can be a little tedious.
Below, two example topologies are shown: the acetylated lysine (ALY) and negatively charged Cys (CYN); treat those as an extension to CHARMM protein force-field. ALY is can be used to model modifications on histone proteins, while CYN is supposed to model Cys in zinc-finger motifs where it coordinates Zn2+ ions.
The two topologies below are simple hacks. At no point am I claiming that they are 'correct' in any way – but they provide a starting point for any improvements one wishes to make.
Edit: I recently bumped into a paper called Force field parameters for the simulation of modified histone tails where quantum calculations are done to obtain CHARMM parameters for the modified aminoacid residues. This could be a more reliable set of parameters than what I give here for acetylated-lysine; however, the aren't any parameter files in the SI of the paper or anywhere else I looked...
Acetylated lysine (resname ALY)
# edit aminoacids.rtp and add the following lines
[ ALY ] ; acetylated lysine
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CT2 -0.18 7
HG1 HA 0.09 8
HG2 HA 0.09 9
CD CT2 -0.18 10
HD1 HA 0.09 11
HD2 HA 0.09 12
CE CT2 0.07 13 ; charge as per the CA atom
HE1 HA 0.09 14
HE2 HA 0.09 15
NZ NH1 -0.47 16 ; type changed from NH2 to NH1
HZ H 0.31 17 ; charge as per peptide bond
C C 0.51 18
O O -0.51 19
CH3 CT3 -0.270 20
HH31 HA 0.090 21
HH32 HA 0.090 22
HH33 HA 0.090 23
CH C 0.510 24
OH O -0.510 25
[ bonds ]
CB CA
CG CB
CD CG
CE CD
NZ CE
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CG HG1
CG HG2
CD HD1
CD HD2
CE HE1
CE HE2
O C
NZ HZ
CH CH3
CH NZ
CH3 HH31
CH3 HH32
CH3 HH33
OH CH
[ impropers ]
N -C CA HN
C CA +N O
;[ cmap ]
; -C N CA C +N
aminoacids.hdb
ALY 8
1 1 HN N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
2 6 HG CG CD CB
2 6 HD CD CE CG
2 6 HE CE NZ CD
1 1 HZ NZ CE CD
3 4 HH3 CH3 CH OH
# edit residuetypes.dat and add the following line
ALY Protein
[ CYN ]; negative cysteine, JD: the partial charge on SG is completely made up
[ atoms ]
N NH1 -0.470 1 ; |
HN H 0.310 2 ; HN-N
CA CT1 0.070 3 ; | HB1
HA HB 0.090 4 ; | |
CB CT2 -0.280 5 ; HA-CA--CB--SG-
HB1 HA 0.050 6 ; | |
HB2 HA 0.050 7 ; | HB2
SG S -0.820 8 ; O=C
C C 0.510 9
O O -0.510 10
[ bonds ]
CB CA
SG CB
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
SG HG1
O C
[ impropers ]
N -C CA HN
C CA +N O
aminoacids.hdb
CYN 3
1 1 HN N -C CA
1 5 HA CA N C CB
2 6 HB CB SG CA
# edit residuetypes.dat and add the following line
CYN Protein
Below, two example topologies are shown: the acetylated lysine (ALY) and negatively charged Cys (CYN); treat those as an extension to CHARMM protein force-field. ALY is can be used to model modifications on histone proteins, while CYN is supposed to model Cys in zinc-finger motifs where it coordinates Zn2+ ions.
The two topologies below are simple hacks. At no point am I claiming that they are 'correct' in any way – but they provide a starting point for any improvements one wishes to make.
Edit: I recently bumped into a paper called Force field parameters for the simulation of modified histone tails where quantum calculations are done to obtain CHARMM parameters for the modified aminoacid residues. This could be a more reliable set of parameters than what I give here for acetylated-lysine; however, the aren't any parameter files in the SI of the paper or anywhere else I looked...
Acetylated lysine (resname ALY)
# edit aminoacids.rtp and add the following lines
[ ALY ] ; acetylated lysine
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CT2 -0.18 7
HG1 HA 0.09 8
HG2 HA 0.09 9
CD CT2 -0.18 10
HD1 HA 0.09 11
HD2 HA 0.09 12
CE CT2 0.07 13 ; charge as per the CA atom
HE1 HA 0.09 14
HE2 HA 0.09 15
NZ NH1 -0.47 16 ; type changed from NH2 to NH1
HZ H 0.31 17 ; charge as per peptide bond
C C 0.51 18
O O -0.51 19
CH3 CT3 -0.270 20
HH31 HA 0.090 21
HH32 HA 0.090 22
HH33 HA 0.090 23
CH C 0.510 24
OH O -0.510 25
[ bonds ]
CB CA
CG CB
CD CG
CE CD
NZ CE
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CG HG1
CG HG2
CD HD1
CD HD2
CE HE1
CE HE2
O C
NZ HZ
CH CH3
CH NZ
CH3 HH31
CH3 HH32
CH3 HH33
OH CH
[ impropers ]
N -C CA HN
C CA +N O
;[ cmap ]
; -C N CA C +N
aminoacids.hdb
ALY 8
1 1 HN N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
2 6 HG CG CD CB
2 6 HD CD CE CG
2 6 HE CE NZ CD
1 1 HZ NZ CE CD
3 4 HH3 CH3 CH OH
# edit residuetypes.dat and add the following line
ALY Protein
Negatively charged cysteine (resname CYN)
# edit aminoacids.rtp and add the following lines[ CYN ]; negative cysteine, JD: the partial charge on SG is completely made up
[ atoms ]
N NH1 -0.470 1 ; |
HN H 0.310 2 ; HN-N
CA CT1 0.070 3 ; | HB1
HA HB 0.090 4 ; | |
CB CT2 -0.280 5 ; HA-CA--CB--SG-
HB1 HA 0.050 6 ; | |
HB2 HA 0.050 7 ; | HB2
SG S -0.820 8 ; O=C
C C 0.510 9
O O -0.510 10
[ bonds ]
CB CA
SG CB
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
SG HG1
O C
[ impropers ]
N -C CA HN
C CA +N O
aminoacids.hdb
CYN 3
1 1 HN N -C CA
1 5 HA CA N C CB
2 6 HB CB SG CA
# edit residuetypes.dat and add the following line
CYN Protein