From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Wed Mar 24 2004 - 11:55:54 CST
Le Mercredi 24 Mars 2004 17:04, Satyavani Vemparala a écrit :
> I am trying to setup systems to compute the relative binding affinities of
> two ligands L1 and L2 to a receptor R.
> In the examples given in the tutorial on NAMD website, the dual topology
> is represented through a hybrid molecule whose residue is defined in the
> RTF file for CHARMM. In this hybrid molecule, there is connectivity
> between initial and final states
> But for my problem, the two ligands L1 and L2 are not connected, in this
> case how do i define a hybrid molecule 'residue' for the CHARMM to
> generate the exclusion lists?
I don't know how you can tell CHARMM to generate exclusions between different
residues. Maybe someone on the list with more experience of that software
than I have will be able to help.
One thing you could do is define a single residue containing both ligands
joined by a "fake" bond with zero force constant. This is rather ugly.
A cleaner approach is to postprocess the PSF file to add the required
exclusions. A happy coincidence is that I'm presently working on a utility
designed to make PSF files suitable for alchemical transformations. I hope to
build a fully functional version next week. It is designed to allow people to
setup alchemical FEP runs without using CHARMM (e.g. using only psfgen), but
it would solve your problem too.
-- Jérôme Hénin Equipe Dynamique des Assemblages Membranaires Université Henri Poincaré / CNRS UMR 7565 B.P. 239 54506 Vandoeuvre-lès-Nancy Cedex Tel : (33) 3 83 68 43 95 Fax : (33) 3 83 68 43 71 http://www.edam.uhp-nancy.fr/
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