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

Esteban Gabriel Vega Hissi egvega at gmail.com
Tue Nov 16 07:47:54 CET 2010


Justin,

Regarding the charges you mention, what do you think about RESP charges for
this kind of compounds (drugs) parameterization?

Best wishes

Esteban

--
On Mon, Nov 15, 2010 at 11:12 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
> Just the $0.02 that I always seem to contribute in these types of
> discussions - the topology you have shown below contains some likely
> problems.  The charges (and massive charge group size) can lead to
> artifacts.  We've got a paper due out soon about the implications of
> incorrect charges, but I would advise you that this topology should *not* be
> used for production simulation.  You'd be better off spending the time to
> properly parameterize the molecule rather than run a bunch of simulations
> and get questionable (at best) or wrong (at worst) results.
>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> -Justin
>
> Olga Ivchenko 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<mailto:
>> 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 <mailto: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
>>
>>
>>
>>
>>     > I still have troubles of starting running md for creatine. For
>>    which I
>>     > created topology using PRODRG programm.
>>     > The only difference between creatine.top and creating.itp is that
>>    creatine
>>     > top has additional lines:
>>     >  #include "ffgmx.itp"
>>     > #include "creatine.itp"
>>     >
>>     > Also please can you tell me where can I get "ffgmx.itp" file?
>>     >
>>     > By trying to run md I am getting an error: Fatal error:
>>     > moleculetype UNK is redefined
>>
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
> --
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