[gmx-users] Proline on OPLSSaa
Mauro Puppett
esagono at hotmail.com
Fri Feb 8 16:23:21 CET 2008
Hi all,
I'm trying to run a simulation of a proline in water tip5p with OPLSaa ff.
The problem is that it has to be an N-acetyl-methoxyproline and i don't know how to add the methoxy.
I've already tryed adding a new molecule to the .rtp file:
[ APR ]
[ atoms ]
N opls_239 -0.776797 1
CA opls_246 -0.158578 2
C1 opls_058 0.954250 3
OS1 opls_062 -0.719990 4
C2 opls_235 0.808979 5
OS opls_059 -0.616492 6
CD opls_245 -0.150278 7
CB opls_136 -0.404838 8
HB1 opls_140 0.243450 9
CG opls_136 -0.450709 10
HB2 opls_140 0.226125 11
HG1 opls_140 0.223126 12
HG2 opls_140 0.242534 13
HD1 opls_140 0.239430 14
HD2 opls_140 0.239331 15
HA opls_140 0.262623 16
CE opls_468 -0.252649 17
HE1 opls_469 0.216104 18
HE2 opls_469 0.214466 19
HE3 opls_469 0.212312 20
OB opls_236 -0.606932 21
CF opls_135 -0.687405 22
HF1 opls_140 0.262125 23
HF2 opls_140 0.224449 24
HF3 opls_140 0.255303 25
[ bonds ]
N CD
N C2
C2 OB
C2 CF
CF HF1
CF HF2
CF HF3
CD HD1
CD HD2
CD CG
CG HG1
CG HG2
CG CB
CB HB1
CB HB2
CB CA
CA N
CA HA1
CA C1
C1 OS
C1 OS1
OS1 CE
CE HE1
CE HE1
CE HE3
and it works fine till i run grompp which says:
ERROR 0 [file "proline.top", line 182]:
No default Ryckaert-Bell. types
ERROR 0 [file "proline.top", line 191]:
No default Ryckaert-Bell. types
ERROR 0 [file "proline.top", line 193]:
No default Ryckaert-Bell. types
ERROR 0 [file "proline.top", line 201]:
No default Ryckaert-Bell. types
This is my .top file:
; This is your topology file
; %E
;
; Include forcefield parameters
#include "ffoplsaa.itp"
; Include water topology
#include "tip5p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 opls_239 1 APR N 1 -0.776797 14.0067 ; qtot -0.7768
2 opls_246 1 APR CA 2 -0.158578 12.011 ; qtot -0.9354
3 opls_058 1 APR C1 3 0.95425 12.011 ; qtot 0.01887
4 opls_062 1 APR OS1 4 -0.71999 15.9994 ; qtot -0.7011
5 opls_235 1 APR C2 5 0.808979 12.011 ; qtot 0.1079
6 opls_059 1 APR OS 6 -0.616492 15.9994 ; qtot -0.5086
7 opls_245 1 APR CD 7 -0.150278 12.011 ; qtot -0.6589
8 opls_136 1 APR CB 8 -0.404838 12.011 ; qtot -1.064
9 opls_140 1 APR HB1 9 0.24345 1.008 ; qtot -0.8203
10 opls_136 1 APR CG 10 -0.450709 12.011 ; qtot -1.271
11 opls_140 1 APR HB2 11 0.226125 1.008 ; qtot -1.045
12 opls_140 1 APR HG1 12 0.223126 1.008 ; qtot -0.8218
13 opls_140 1 APR HG2 13 0.242534 1.008 ; qtot -0.5792
14 opls_140 1 APR HD1 14 0.23943 1.008 ; qtot -0.3398
15 opls_140 1 APR HD2 15 0.239331 1.008 ; qtot -0.1005
16 opls_140 1 APR HA 16 0.262623 1.008 ; qtot 0.1622
17 opls_468 1 APR CE 17 -0.252649 12.011 ; qtot -0.09048
18 opls_469 1 APR HE1 18 0.216104 1.008 ; qtot 0.1256
19 opls_469 1 APR HE2 19 0.214466 1.008 ; qtot 0.3401
20 opls_469 1 APR HE3 20 0.212312 1.008 ; qtot 0.5524
21 opls_236 1 APR OB 21 -0.606932 15.9994 ; qtot -0.05453
22 opls_135 1 APR CF 22 -0.687405 12.011 ; qtot -0.7419
23 opls_140 1 APR HF1 23 0.262125 1.008 ; qtot -0.4798
24 opls_140 1 APR HF2 24 0.224449 1.008 ; qtot -0.2554
25 opls_140 1 APR HF3 25 0.255303 1.008 ; qtot -6.101e-05
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 5 1
1 7 1
2 3 1
2 8 1
3 4 1
3 6 1
4 17 1
5 21 1
5 22 1
7 10 1
7 14 1
7 15 1
8 9 1
8 10 1
8 11 1
10 12 1
10 13 1
17 18 1
17 20 1
22 23 1
22 24 1
22 25 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
1 6 1
1 9 1
1 11 1
1 12 1
1 13 1
1 23 1
1 24 1
1 25 1
2 12 1
2 13 1
2 14 1
2 15 1
2 17 1
2 21 1
2 22 1
3 5 1
3 7 1
3 9 1
3 10 1
3 11 1
3 18 1
3 20 1
4 8 1
5 8 1
5 10 1
5 14 1
5 15 1
6 8 1
6 17 1
7 9 1
7 11 1
7 21 1
7 22 1
8 14 1
8 15 1
9 12 1
9 13 1
11 12 1
11 13 1
12 14 1
12 15 1
13 14 1
13 15 1
21 23 1
21 24 1
21 25 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 5 1
2 1 7 1
5 1 7 1
1 2 3 1
1 2 8 1
3 2 8 1
2 3 4 1
2 3 6 1
4 3 6 1
3 4 17 1
1 5 21 1
1 5 22 1
21 5 22 1
1 7 10 1
1 7 14 1
1 7 15 1
10 7 14 1
10 7 15 1
14 7 15 1
2 8 9 1
2 8 10 1
2 8 11 1
9 8 10 1
9 8 11 1
10 8 11 1
7 10 8 1
7 10 12 1
7 10 13 1
8 10 12 1
8 10 13 1
12 10 13 1
4 17 18 1
4 17 20 1
18 17 20 1
5 22 23 1
5 22 24 1
5 22 25 1
23 22 24 1
23 22 25 1
24 22 25 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
5 1 2 3 3
5 1 2 8 3
7 1 2 3 3
7 1 2 8 3
2 1 5 21 3
2 1 5 22 3
7 1 5 21 3
7 1 5 22 3
2 1 7 10 3
2 1 7 14 3
2 1 7 15 3
5 1 7 10 3
5 1 7 14 3
5 1 7 15 3
1 2 3 4 3
1 2 3 6 3
8 2 3 4 3
8 2 3 6 3
1 2 8 9 3
1 2 8 10 3
1 2 8 11 3
3 2 8 9 3
3 2 8 10 3
3 2 8 11 3
2 3 4 17 3
6 3 4 17 3
3 4 17 18 3
3 4 17 20 3
1 5 22 23 3
1 5 22 24 3
1 5 22 25 3
21 5 22 23 3
21 5 22 24 3
21 5 22 25 3
1 7 10 8 3
1 7 10 12 3
1 7 10 13 3
14 7 10 8 3
14 7 10 12 3
14 7 10 13 3
15 7 10 8 3
15 7 10 12 3
15 7 10 13 3
2 8 10 7 3
2 8 10 12 3
2 8 10 13 3
9 8 10 7 3
9 8 10 12 3
9 8 10 13 3
11 8 10 7 3
11 8 10 12 3
11 8 10 13 3
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
%E in water
[ molecules ]
; Compound #mols
Protein 1
SOL 2390
Can somebody pelase tell what I'm doing wrong?
Thanks in advance
Mauro Puppett
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