[gmx-users] Re: still can not run md for creatine
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Nov 15 23:44:24 CET 2010
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.ivchenko at 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 dava at 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<vvchaban at 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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