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

[Anirban Ghosh]

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



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