[gmx-users] Problem with protein in lipid bilayer simulation

Justin A. Lemkul jalemkul at vt.edu
Fri May 8 16:58:29 CEST 2009

Anirban Ghosh wrote:
> Hi ALL,
> I am trying to run a simulation of a GPCR protein in a POPC bilayer. I 
> have got the lipid.itp file and trying to use the ffgmxbon.itp and 
> ffgmxnb.itp for the simulation. I am getting errors like "LC3 atom not 
> found", "HC atom not found" after incorporating several changes in the 
> itp files according to previous posts with same problem. I think 
> ffgmx.itp has only the parameters for the lipid atoms. So I tried to use 
> two FFs simultaneously, ffgmx.itp and ffG53a1.itp. But in that case I 
> get the error of parameter overwriting. I have tried all the suggestions 
> from the mail list but still cannot run grompp successfully. I shall be 
> glad if someone can briefly explain how to run grompp to generate a tpr 
> file for this protein + POPC + water simulation.
> Any suggestion is welcome.

My tutorial will walk you through this.  It is linked from:



> Regards,
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
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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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