Re: Thermodynamic integration question

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Sep 07 2015 - 01:44:15 CDT

Hi Randy,

Have a look at the Mutator plugin of VMD, as well as the hybrid topology
file in the VMD installation directory:
vmd/plugins/noarch/tcl/readcharmmtop1.1/top_all27_hybrid.inp

Best,
Jerome

On 6 September 2015 at 06:28, Randall Hall <randall.hall_at_dominican.edu>
wrote:

> Dear List Members,
> Is there a sample pdb input file for a thermodynamic integration? If
> not, my question is related to the structure of the pdb file. If I
> understand the documentation, if I wish to mutate LYS to ARG, for example,
> I need to create a new residue that has two side chains attached to the
> same NH-CH-CO backbone structure. Is this correct?
>
> Randy
>
>
>
> Randall Hall
> Lillian L.Y. Wang Yin, Ph.D. Endowed Professor of Chemistry
> Chair, Department of Natural Sciences and Mathematics
> Dominican University of California
> randall.hall_at_dominican.edu
> Phone: 415-482-1911
> Fax: 415-482-1972
>
>
>
>
>
>
>
>

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:17 CST