Re: how to make dual-hybrid topology?

From: Chris Chipot (
Date: Mon Feb 13 2006 - 08:31:45 CST


we have a dual-topology data base of the 19 x 20 / 2 amino-acid
hybrids, that we have not included yet on the NAMD webpage, and
distribute right now upon request.

With this data base, PSFgen and alchemify (a utilitary that builds
the correct PSF files, bereft of superfluous angles/torsions), you
won't need CHARMM to set up your alchemical FEP calculations.


Chris Chipot

Indrajaya wrote:

>Dear NAMD users,
>I'm Indrajaya, student of Bandung Institute of Technology, Indonesia. I'm using NAMD to do my research. I want to use alchemical free enery perturbation feature in NAMD but I don't have a dual-topology hybrid of my amino acid topology (alanine and glutamic acid). From the tutorial in NAMD web site about setting up alchemical free energy perturbation calculation in NAMD, it state that CHARMM can make this kind topology. Unfortunely, we don't have CHARMM program in our laboratory. Can anybody guide me how to
>make this topology without CHARMM?
>Thank you very much for your attention. I'm looking forward to hearing you soon.

Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97
B.P. 239 Fax: (33) 3-83-68-43-87
54506 Vandoeuvre-lès-Nancy Cedex


      To sin by silence when we should protest makes cowards out of men
                                                    Ella Wheeler Wilcox

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