VMD-L Mailing List

From: Glenn Johnson (gjohnson_at_srrc.ars.usda.gov)
Date: Mon Mar 21 2005 - 12:08:26 CST

On Mon, 2005-03-21 at 17:09 +0000, Nuno R. L. Ferreira wrote:

> > I have converted a .dcd file from NAMD to a Gromacs .trr file. When I
> > try to use, for example, g_covar, the command fails because it needs
> > a .tpr file. According to the help blurb for g_covar, that file is a
> > "Structure+mass(db)" file but can be in .pdb format. Is there a way to
> > generate this file? If I need to edit it manually, in what column of
> > the .pdb file would I place the mass values?
> >
>
> Have you tryed to save a single frame of your trajectory in .pdb, and use it
> as input for g_covar?
> Nuno

I just did and it seems to work. So apparently, the mass values do not
have to be in the PDB after all.

Thanks. 

-- 
Glenn Johnson <gjohnson_at_srrc.ars.usda.gov>
U. S. Department of Agriculture