[gmx-users] swiss param query,

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 12 18:09:26 CEST 2010

ram bio wrote:
> Dear Gromacs Users,
> I have generated the topology and parameters files for my ligand
> through swiss param site. Now i am trying to run a simulation of
> protein ligand complex in POPC bilayer using OPLS force field in
> Gromacs, but when I am using the grompp command in gromacs for tpr
> generation I am getting an error as follows:

I've not used SwissParam, but it advertises itself as a means to generate CHARMM 
parameters, not OPLS.  So it sounds like you're mixing force fields, which is 
not appropriate.

> Atomtype C5A not found
> Please let me know your suggestions, to correct this error, I have
> included ligand.itp in the topology file of the protein.

The ligand.itp file probably utilizes atomtypes that are not present in OPLS-AA. 
  This should be your first hint that you're doing something you shouldn't.


> Thanks,
> ram
> grompp -f mdions.mdp -c combi.gro -p topol.top -o combi.tpr
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'cpp'
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14#
> checking input for internal consistency...
> NOTE 1 [file mdions.mdp, line unknown]:
>   The Berendsen thermostat does not generate the correct kinetic energy
>   distribution. You might want to consider using the V-rescale thermostat.
> processing topology...
> Opening library file
> /usr/local/gromacs-4.0.7-single/share/gromacs/top/ffoplsaa.itp
> Opening library file
> /usr/local/gromacs-4.0.7-single/share/gromacs/top/ffoplsaanb.itp
> Opening library file
> /usr/local/gromacs-4.0.7-single/share/gromacs/top/ffoplsaabon.itp
> Generated 348195 of the 348195 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 348005 of the 348195 1-4 parameter combinations
> Opening library file /usr/local/gromacs-4.0.7-single/share/gromacs/top/tip3p.itp
> Opening library file /usr/local/gromacs-4.0.7-single/share/gromacs/top/ions.itp
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: toppush.c, line: 947
> Fatal error:
> Atomtype C5A not found


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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