[gmx-users] Re: still can not run md for creatine
Justin A. Lemkul
jalemkul at vt.edu
Tue Nov 16 03:12:29 CET 2010
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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