[gmx-users] Add new residue to forcefield
fatemeh ramezani
fr_750 at yahoo.com
Tue Dec 16 10:58:39 CET 2014
Hi Dear gmx-users
I want to simulate a tripeptide contain hydroxyprolin by OPLSAA. I added hydroxyprolin parameters as
follow:
in .hdb file :
HYP 5
1 5 HA CA N C CB
2 6 HB CB CG CA
1 6 HG CG CD CB
1 6 HD CD N CG
1 4 HO OH CG CD
in aminoacids.c.tdb file:
[ HYP-COO- ]
[ replace ]
CA CA opls_285 12.011 -0.09
C C opls_271 12.011 0.7
O O1 opls_272 15.9994 -0.8
OXT O2 opls_272 15.9994 -0.8
[ add ]
2 8 O C CA N
opls_272 15.9994 -0.8
[ impropers ]
CA O1 C O2 improper_O_C_X_Y
[ HYP-ZWITTERION_COO- ]
[ replace ]
CA CA opls_246 12.011 0.13
C C opls_271 12.011 0.7
O O1 opls_272 15.9994 -0.8
OXT O2 opls_272 15.9994 -0.8
[ add ]
2 8 O C CA N
opls_272 15.9994 -0.8
[ impropers ]
CA O1 C O2 improper_O_C_X_Y
in aminoacids.n.tdb file:
[ HYP-COO- ]
[ replace ]
CA CA opls_285 12.011 -0.09
C C opls_271 12.011 0.7
O O1 opls_272 15.9994 -0.8
OXT O2 opls_272 15.9994 -0.8
[ add ]
2 8 O C CA N
opls_272 15.9994 -0.8
[ impropers ]
CA O1 C O2 improper_O_C_X_Y
[ HYP-ZWITTERION_COO- ]
[ replace ]
CA CA opls_246 12.011 0.13
C C opls_271 12.011 0.7
O O1 opls_272 15.9994 -0.8
OXT O2 opls_272 15.9994 -0.8
[ add ]
2 8 O C CA N
opls_272 15.9994 -0.8
[ impropers ]
CA O1 C O2 improper_O_C_X_Y
in aminoacids.rtp file:
[HYP]
[ atoms ]
N opls_239 -0.140 1
CA opls_246 0.010 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_136 -0.120 3
HG1 opls_140 0.060 3
OH opls_167 -0.683 3
HO opls_168 0.435 3
CD opls_245 -0.050 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ bonds ]
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG OH
OH HO
CG CD
CD HD1
CD HD2
CD N
C O
-C N
[ impropers ]
-C CA N CD improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
in ffbonded.itp file:
[ bondtypes ]
CG OH 2 0.144 6100000.0 ;
OH HO 2 0.100 15700000.0 ;
[ angletypes ]
; i j k func th0 cth
CG CB OH 2 109.5 520.0
OH CG CD 2 109.5 520.0
CG OH HO 2 109.5 450.0
[ dihedraltypes ]
CG CB CD OH 1 35.3 334.8
CB CG OH HO 1 0.0 1.3 3
After pdb2gmx command top file was generated:
...
; Include forcefield parameters
#include "./oplsaa.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 22 PRO rtp PRO q +0.9
1 opls_309 22 PRO N 1 -0.2 14.0067 ; qtot -0.2
2 opls_310 22 PRO H1 1 0.31 1.008 ; qtot 0.11
3 opls_310 22 PRO H2 1 0.31 1.008 ; qtot 0.42
4 opls_246 22 PRO CA 1 0.13 12.011 ; qtot 0.55
5 opls_140 22 PRO HA 1 0.06 1.008 ; qtot 0.61
6 opls_136 22 PRO CB 2 -0.12 12.011 ; qtot 0.49
7 opls_140 22 PRO HB1 2 0.06 1.008 ; qtot 0.55
8 opls_140 22 PRO HB2 2 0.06 1.008 ; qtot 0.61
9 opls_136 22 PRO CG 3 -0.12 12.011 ; qtot 0.49
10 opls_140 22 PRO HG1 3 0.06 1.008 ; qtot 0.55
11 opls_140 22 PRO HG2 3 0.06 1.008 ; qtot 0.61
12 opls_296 22 PRO CD 4 0.17 12.011 ; qtot 0.78
13 opls_140 22 PRO HD1 4 0.06 1.008 ; qtot 0.84
14 opls_140 22 PRO HD2 4 0.06 1.008 ; qtot 0.9
15 opls_235 22 PRO C 5 0.5 12.011 ; qtot 1.4
16 opls_236 22 PRO O 5 -0.5 15.9994 ; qtot 0.9
; residue 23 HYP rtp HYP q -0.4
17 opls_239 23 HYP N 6 -0.14 14.0067 ; qtot 0.76
18 opls_246 23 HYP CA 6 0.01 12.011 ; qtot 0.77
19 opls_140 23 HYP HA 6 0.06 1.008 ; qtot 0.83
20 opls_136 23 HYP CB 7 -0.12 12.011 ; qtot 0.71
21 opls_140 23 HYP HB1 7 0.06 1.008 ; qtot 0.77
22 opls_140 23 HYP HB2 7 0.06 1.008 ; qtot 0.83
23 opls_136 23 HYP CG 8 -0.12 12.011 ; qtot 0.71
24 opls_140 23 HYP HG 8 0.06 1.008 ; qtot 0.77
25 opls_167 23 HYP OH 8 -0.683 15.9994 ; qtot 0.087
26 opls_168 23 HYP HO 8 0.435 1.008 ; qtot 0.522
27 opls_245 23 HYP CD 9 -0.05 12.011 ; qtot 0.472
28 opls_140 23 HYP HD 9 0.06 1.008 ; qtot 0.532
29 opls_235 23 HYP C 10 0.5 12.011 ; qtot 1.032
30 opls_236 23 HYP O 10 -0.5 15.9994 ; qtot 0.532
; residue 24 GLY rtp GLY q -0.9
31 opls_238 24 GLY N 11 -0.5 14.0067 ; qtot 0.032
32 opls_241 24 GLY H 11 0.3 1.008 ; qtot 0.332
33 opls_298 24 GLY CA 11 0.09 12.011 ; qtot 0.422
34 opls_140 24 GLY HA1 11 0.06 1.008 ; qtot 0.482
35 opls_140 24 GLY HA2 11 0.06 1.008 ; qtot 0.542
36 opls_271 24 GLY C 12 0.7 12.011 ; qtot 1.242
37 opls_272 24 GLY O1 12 -0.8 15.9994 ; qtot 0.442
38 opls_272 24 GLY O2 12 -0.8 15.9994 ; qtot -0.358
.
.
.
When I grompp, I get this error :
ERROR 1 [file topol.top, line 258]:
No default Angle types
In topol.top line 258 contain atoms 25 23 27 that are atoms OH CG CD and I added the angle between them in [angletypes] section in ffbonded.itp file.
I would be grateful if anyone could shed some light on the origin of
this error, and on what I can do to correct it.
Fatemeh Ramezani
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