[gmx-users] PRODRG - .itp file
Luciane Vieira de Mello
mello at cenargen.embrapa.br
Tue Dec 17 19:32:39 CET 2002
Dear all,
I 've been using the excellent PRODRG server with success recently, but
I'm having some unexpected problems this time.
My ligand is 2-phosphoglycerate. The only change I made to the
PRODRG-derived parameters (the .itp file) was to make the three chemically
equivalent atoms the same in terms of charge etc. The problem is that
after energy minimization with these parameters, the phosphate group
becomes distorted. The distortion is quite marked - see attached snapshot
and pdb file. I've tried various things but I always get the distortion.
The only thing in the itp file which looks strange is the double entry for
one of the dihedrals
6 5 2 1 1 0.0 1.0 3 0.0 1.0 3 ; DI C2 O1P P
O4P
6 5 2 1 1 0.0 3.1 2 0.0 3.1 2 ; DI C2 O1P P
O4P
However, when I delete either one the distorion is much worse!
Can anybody help?
Thanks in advance
+-------------------------------------------------------------------------+
| Dra. Luciane Vieira de Mello Rigden |
| e-mail: mello at cenargen.embrapa.br |
| Embrapa Recursos Geneticos e Biotecnologia |
| Parque Estacao Biologica | http://www.cenargen.embrapa.br |
| PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741 |
| 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3658 |
+-------------------------------------------------------------------------+
-------------- next part --------------
ATOM 1 O4P DRG 1 15.220 11.270 11.000 1.00 0.00
ATOM 2 P DRG 1 13.650 10.900 11.140 1.00 0.00
ATOM 3 O2P DRG 1 13.760 9.440 11.240 1.00 0.00
ATOM 4 O3P DRG 1 13.140 11.530 9.910 1.00 0.00
ATOM 5 O1P DRG 1 13.090 11.510 12.510 1.00 0.00
ATOM 6 C2 DRG 1 12.250 12.690 12.560 1.00 0.00
ATOM 7 C1 DRG 1 11.340 12.860 13.840 1.00 0.00
ATOM 8 O2 DRG 1 10.520 13.850 13.800 1.00 0.00
ATOM 9 O1 DRG 1 11.410 12.130 14.820 1.00 0.00
ATOM 10 C3 DRG 1 13.130 13.940 12.450 1.00 0.00
ATOM 11 O3 DRG 1 12.280 15.090 12.380 1.00 0.00
ATOM 12 HAA DRG 1 11.470 14.700 12.900 1.00 0.00
-------------- next part --------------
[ moleculetype ]
;name nrexcl
2PG 3
;
[ atoms ]
; nr type resnr resid atom cgnr charge
1 OA 1 DRG O4P 1 -1.087
2 P 1 DRG P 1 1.980
3 OM 1 DRG O2P 1 -1.087
4 OM 1 DRG O3P 1 -1.087
5 OS 1 DRG O1P 1 -0.720
6 CH1 1 DRG C2 2 0.000
7 C 1 DRG C1 3 0.270
8 OM 1 DRG O2 3 -0.635
9 OM 1 DRG O1 3 -0.635
10 CH2 1 DRG C3 4 0.150
11 OA 1 DRG O3 4 -0.548
12 HO 1 DRG HAA 4 0.398
[ bonds ]
;ai aj fu c0 c1
1 2 1 0.161 251040.0 0.161 251040.0 ; O4P P
2 3 1 0.148 376560.0 0.148 376560.0 ; P O2P
2 4 1 0.148 376560.0 0.148 376560.0 ; P O3P
2 5 1 0.161 251040.0 0.161 251040.0 ; P O1P
5 6 1 0.143 334720.0 0.143 334720.0 ; O1P C2
6 7 1 0.153 334720.0 0.153 334720.0 ; C2 C1
6 10 1 0.153 334720.0 0.153 334720.0 ; C2 C3
7 8 1 0.125 418400.0 0.125 418400.0 ; C1 O2
7 9 1 0.125 418400.0 0.125 418400.0 ; C1 O1
10 11 1 0.143 334720.0 0.143 334720.0 ; C3 O3
11 12 1 0.100 313800.0 0.100 313800.0 ; O3 HAA
[ pairs ]
;ai aj fu c0 c1
1 6 1 ; O4P C2
2 7 1 ; P C1
2 10 1 ; P C3
3 6 1 ; O2P C2
4 6 1 ; O3P O1P
5 8 1 ; O1P C2
5 9 1 ; O1P C2
5 11 1 ; O1P C2
6 12 1 ; C2 C1
7 11 1 ; C2 C3
8 10 1 ; C1 O2
9 10 1 ; C1 O1
[ angles ]
;ai aj ak fu c0 c1
1 2 3 1 109.6 397.5 109.6 397.5 ; O4P P O2P
1 2 4 1 109.6 397.5 109.6 397.5 ; O4P P O3P
3 2 4 1 109.6 397.5 109.6 397.5 ; O2P P O3P
1 2 5 1 109.6 397.5 109.6 397.5 ; O4P P O1P
3 2 5 1 109.6 397.5 109.6 397.5 ; O2P P O1P
4 2 5 1 109.6 397.5 109.6 397.5 ; O3P P O1P
2 5 6 1 120.0 397.5 120.0 397.5 ; P O1P C2
5 6 7 1 109.5 460.2 109.5 460.2 ; O1P C2 C1
5 6 10 1 109.5 460.2 109.5 460.2 ; O1P C2 C3
7 6 10 1 109.5 460.2 109.5 460.2 ; C1 C2 C3
6 7 8 1 117.0 502.1 117.0 502.1 ; C2 C1 O2
6 7 9 1 117.0 502.1 117.0 502.1 ; C2 C1 O1
8 7 9 1 126.0 502.1 126.0 502.1 ; O2 C1 O1
6 10 11 1 109.5 460.2 109.5 460.2 ; C2 C3 O3
10 11 12 1 109.5 397.5 109.5 397.5 ; C3 O3 HAA
[ dihedrals ]
;ai aj ak al fu c0 c1 m c0 c1 m
7 6 9 8 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C1 C2 O1 O2
2 1 3 4 2 35.3 836.8 0 35.3 836.8 0 ; IDI P O4P O2P O3P
6 5 10 7 2 35.3 836.8 0 35.3 836.8 0 ; IDI C2 O1P C3 C1
6 5 2 1 1 0.0 1.0 3 0.0 1.0 3 ; DI C2 O1P P O4P
; 6 5 2 1 1 0.0 3.1 2 0.0 3.1 2 ; DI C2 O1P P O4P
2 5 6 10 1 0.0 1.3 3 0.0 1.3 3 ; DI P O1P C2 C3
5 6 7 9 1 0.0 0.4 6 0.0 0.4 6 ; DI O1P C2 C1 O1
11 10 6 5 1 0.0 5.9 3 0.0 5.9 3 ; DI O3 C3 C2 O1P
6 10 11 12 1 0.0 1.3 3 0.0 1.3 3 ; DI C2 C3 O3 HAA
More information about the gromacs.org_gmx-users
mailing list