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

[Justin A. Lemkul]

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:

http://wiki.gromacs.org/index.php/Membrane_Simulations

-Justin

> Regards,
> 
> 
>  
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
> 
> 
> ------------------------------------------------------------------------
> Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! 
> Edition * Click here! 
> <http://in.rd.yahoo.com/tagline_firefox_1/*http://downloads.yahoo.com/in/firefox/?fr=om_email_firefox> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================