[gmx-users] FEP doubts

[Diego Nolasco]

Dear gmx users,
I am attempting to calculate binding free energy of a protein-ligand
complex, but I'm facing some doubts.
Is it possible to use the gromos96 force field instead of opls?
Am I doing all the need type/typeB conversions just turning the atoms charge
to 0 (zero)?
Should I do any modification in [bonds], [pairs], [angles] or [dihedrals]?
Should I perform all these modifications just in the ligand topology or in
the protein-ligand complex topology?

Thanks a lot,
Diego.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080529/66c3b5c6/attachment.html>