[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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