VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Mon Mar 21 2005 - 12:22:52 CST

On Mon, 21 Mar 2005 10:39:00 -0600 Glenn Johnson wrote:

> On Wed, 2005-02-23 at 21:29 +0100, Axel Kohlmeyer wrote:
>
> > hi,
> >
> > just one remark: the gromacs plugin of the latest VMD (1.8.3)
> > should be able to write proper .trr trajectory files
> > (exactly to be able to use the gromacs tools for analysis).
> > you may prefer those over .pdb trajectories as they are binary
> > and thus are read _much_ faster.
> >
> > axel.

> 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

there is a tool pdb2gmx, that will create a topology file from
your pdb file (interactively) and then you can create a matching
.tpr file from it using grompp. these are basically the the steps
you need to set up an md.

> "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?

try http://www.rcsb.org/pdb/info.html

axel.

>
> Thanks.
>
> >>> "JG" == Justin Gullingsrud <justinrocks_at_gmail.com> writes:
>
> > JG> I've used the Gromacs programs g_covar and g_anaeig to perform
> > JG> analysis of NAMD-generated trajectory files by first converting the
> > JG> trajectory to sequential pdb format. You can do this in VMD by simply
> > JG> loading the dcd file and saving it as a pdb, but there is one caveat:
> > JG> you must change all the "END" lines to "ENDMDL", or g_covar will
> > JG> crash.
> >
> > JG> Hope this helps,
> > JG> Justin
>
> --
> Glenn Johnson <gjohnson_at_srrc.ars.usda.gov>
> U. S. Department of Agriculture
> 

--
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Axel Kohlmeyer      e-mail:  axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                   http://www.theochem.ruhr-uni-bochum.de
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If you make something idiot-proof, the universe creates a better idiot.