[gmx-users] Re: still can not run md for creatine

Vitaly Chaban vvchaban at gmail.com
Mon Nov 15 20:22:35 CET 2010


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
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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