Re: [AMBER] VMD-Chamber interface

From: Crowley, Michael <Michael.Crowley.nrel.gov>
Date: Wed, 29 Jun 2011 14:43:47 -0600

Hi Mo,
It is on the to-do list to contact the VMD folks to accommodate the
changes to the prmtop that chamber produces.

In the meantime you cannot use that prmtop with vmd.

The way to visualize is to use either the charmm psf and then the amber
trajectory, or to use a pdb first and then read the amber trajectory.

Mike

-- 
Michael F. Crowley, Ph.D.
Principal Scientist, Biomolecular Sciences Division
National Renewable Energy Laboratory
1617 Cole Blvd.
Golden, CO 80401
303-384-6345 office
303-887=0149 cell
On 6/29/11 2:20 PM, "Mo Chen" <mc842.cornell.edu> wrote:
>Dear Amber Users/Developers,
>I found VMD could not read in the *.prmtop file that is generated, and I
>have noticed in AmberTools tutorial that:
>
>Third party scripts and/or tools which do not correctly parse the
>extensible
>prmtop format
>may have issues with a chamber-generated prmtop file.
>
>So I wonder if there might have been a way to solve this problem?
>
>Best,
>Mo Chen
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Received on Wed Jun 29 2011 - 14:00:04 PDT