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

Pawan Kumar pawan.chinari at gmail.com
Tue May 12 06:49:29 CEST 2009

Hi Anirban,

I have also followed Justin sir's tutorial.
You should not remove the OW entries.
You can remove the HW entries for sure and then this will work.


On Tue, May 12, 2009 at 9:45 AM, Anirban Ghosh <anirbanz83 at yahoo.co.in>wrote:

> Hello Justin,
> Thanks a lot for the reply. Your tutorial is indeed very good.
> I followed your tutorial on protein-lipid simulation. I added the
> non-bonded parameters from the lipid.itp file to the ffG53a6nb_lipid.itp
> file. You have told to either delete the atom-type HW entries having zero
> values in the non-bonded section or replace them with H. But the HW values
> are not zero. And they are also present in the "pairlist" section. So should
> I change in this section also? And when I am running the grompp command I am
> getting the error "Atom-type OW not found". So should I also delete the OW
> entries or should I replace them? If replace, then with what? Should I
> replace all the OW and HW entries throughout the ffG53a6nb_lipid.itp file?
> Please advice.
> Regards,
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
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