[gmx-users] swiss param query,

ram bio rmbio861 at gmail.com
Tue Oct 12 16:32:39 CEST 2010

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:

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.



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
Opening library file
Opening library file
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

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