On 16/11/2010 6:22 AM, Vitaly Chaban wrote:
Olga -
What is gromos43a1.ff? I do not remember the files with ff-extension
in gromacs. I am sure you should include the topology files in the
There's a new force field organization in 4.5.x. PRODRG still presumes
the previous organization, which leads to the OP's first symptoms.
However the real issue is not wanting to use the gmx force field at all.
Mark
inverse order as compared to what is below:
1) general FF with atoms, bonds, angles, etc (~ include "gromos43a1.ff");
2) molecule definition, its own atoms, bonds, etc (~ include "creatine.itp")
After that, you'll probably get another error, and it will be more informative.
Good luck!
Vitaly
On Mon, Nov 15, 2010 at 12:09 PM, Olga Ivchenko<olga.ivche...@gmail.com> wrote:
Hey Vitaly,
Thank you for your reply. Here is the files:
itp:
;
;
; This file was generated by PRODRG version AA081006.0504
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comments to d...@davapc1.bioch.dundee.ac.uk
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
;
;
[ moleculetype ]
Name nrexcl
DRG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 DRG OXT 1 -0.701 15.9994
2 C 1 DRG C 1 0.402 12.0110
3 OM 1 DRG O 1 -0.701 15.9994
4 CH2 1 DRG CA 2 0.185 14.0270
5 N 1 DRG N 2 0.468 14.0067
6 CH3 1 DRG CAG 2 0.201 15.0350
7 C 1 DRG CAH 2 0.377 12.0110
8 NZ 1 DRG NAE 2 -0.163 14.0067
9 H 1 DRG HA6 2 0.023 1.0080
10 H 1 DRG HAE 2 0.024 1.0080
11 NZ 1 DRG NAD 2 -0.163 14.0067
12 H 1 DRG HA5 2 0.024 1.0080
13 H 1 DRG HAD 2 0.024 1.0080
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.125 13400000.0 0.125 13400000.0 ; C OXT
2 3 2 0.125 13400000.0 0.125 13400000.0 ; C O
2 4 2 0.153 7150000.0 0.153 7150000.0 ; C CA
5 4 2 0.147 8710000.0 0.147 8710000.0 ; N CA
5 6 2 0.147 8710000.0 0.147 8710000.0 ; N CAG
5 7 2 0.134 10500000.0 0.134 10500000.0 ; N CAH
7 8 2 0.134 10500000.0 0.134 10500000.0 ; CAH NAE
7 11 2 0.134 10500000.0 0.134 10500000.0 ; CAH NAD
8 9 2 0.100 18700000.0 0.100 18700000.0 ; NAE HA6
8 10 2 0.100 18700000.0 0.100 18700000.0 ; NAE HAE
11 12 2 0.100 18700000.0 0.100 18700000.0 ; NAD HA5
11 13 2 0.100 18700000.0 0.100 18700000.0 ; NAD HAD
[ pairs ]
; ai aj fu c0, c1, ...
1 5 1 ; OXT N
2 6 1 ; C CAG
2 7 1 ; C CAH
3 5 1 ; O N
4 8 1 ; CA NAE
4 11 1 ; CA NAD
5 9 1 ; N HA6
5 10 1 ; N HAE
5 12 1 ; N HA5
5 13 1 ; N HAD
6 8 1 ; CAG NAE
6 11 1 ; CAG NAD
8 12 1 ; NAE HA5
8 13 1 ; NAE HAD
9 11 1 ; HA6 NAD
10 11 1 ; HAE NAD
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 126.0 770.0 126.0 770.0 ; OXT C
O
1 2 4 2 117.0 635.0 117.0 635.0 ; OXT C
CA
3 2 4 2 117.0 635.0 117.0 635.0 ; O C
CA
2 4 5 2 109.5 520.0 109.5 520.0 ; C CA
N
4 5 6 2 121.0 685.0 121.0 685.0 ; CA N
CAG
4 5 7 2 122.0 700.0 122.0 700.0 ; CA N
CAH
6 5 7 2 117.0 635.0 117.0 635.0 ; CAG N
CAH
5 7 8 2 120.0 670.0 120.0 670.0 ; N CAH
NAE
5 7 11 2 120.0 670.0 120.0 670.0 ; N CAH
NAD
8 7 11 2 120.0 670.0 120.0 670.0 ; NAE CAH
NAD
7 8 9 2 120.0 390.0 120.0 390.0 ; CAH NAE
HA6
7 8 10 2 120.0 390.0 120.0 390.0 ; CAH NAE
HAE
9 8 10 2 120.0 445.0 120.0 445.0 ; HA6 NAE
HAE
7 11 12 2 120.0 390.0 120.0 390.0 ; CAH NAD
HA5
7 11 13 2 120.0 390.0 120.0 390.0 ; CAH NAD
HAD
12 11 13 2 120.0 445.0 120.0 445.0 ; HA5 NAD
HAD
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 1 3 4 2 0.0 167.4 0.0 167.4 ; imp C OXT
O CA
5 4 6 7 2 0.0 167.4 0.0 167.4 ; imp N CA
CAG CAH
7 5 8 11 2 0.0 167.4 0.0 167.4 ; imp CAH N
NAE NAD
8 7 10 9 2 0.0 167.4 0.0 167.4 ; imp NAE CAH
HAE HA6
11 7 13 12 2 0.0 167.4 0.0 167.4 ; imp NAD CAH
HAD HA5
5 4 2 1 1 0.0 1.0 6 0.0 1.0 6 ; dih N CA
C OXT
2 4 5 7 1 180.0 1.0 6 180.0 1.0 6 ; dih C CA
N CAH
11 7 5 4 1 180.0 33.5 2 180.0 33.5 2 ; dih NAD CAH
N CA
5 7 8 10 1 180.0 33.5 2 180.0 33.5 2 ; dih N CAH
NAE HAE
5 7 11 13 1 180.0 33.5 2 180.0 33.5 2 ; dih N CAH
NAD HAD
And top. I am prettu sure this file is wrong. And I do not know yet how to
modify it correctly:
;
; File 'creatine.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Mon Nov 15 13:24:44 2010
;
; This is your topology file
; it was generated using program:
; pdb2gmx - version 4.5-beta2
; with command line:
; pdb2gmx -f creatine_all_hyd_PRODRGBeta.pdb -o creatine.gro -p
creatine.top
;
#include "creatine.itp"
#include "gromos43a1.ff"
; Include forcefield parameters
;#include "gromos43a1.ff/forcefield.itp"
;"gromos43a1.ff/creatine.itp"
;[ system ]
;[ molecules ]
;DRG 3
2010/11/15 Vitaly Chaban<vvcha...@gmail.com>
Hey, Olga -
Also please can you tell me where can I get "ffgmx.itp" file?
/$gromacs_folder/share/gromacs/top/ffgmx.itp as well as all other
standard topology files are there.
By trying to run md I am getting an error: Fatal error:
moleculetype UNK is redefined
Please post you top and itp files here. Looks like you have 2 creatine
molecules in your topology right now.
Good luck!
Vitaly
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