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

Anirban Ghosh anirbanz83 at yahoo.co.in
Tue May 12 06:15:11 CEST 2009

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.


 Anirban GhoshGrade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India

      Bollywood news, movie reviews, film trailers and more! Go to http://in.movies.yahoo.com/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090512/efb253f1/attachment.html>

More information about the gromacs.org_gmx-users mailing list