VMD-L Mailing List

From: Robin Betz (robin_at_robinbetz.com)
Date: Thu May 17 2018 - 19:45:20 CDT

Hi Jim,

I'll write and send in a patch for this as it's an issue I notice too.
A short-term fix is to just delete the second number on the first line of
the file with a text editor.

R

On Thu, May 17, 2018 at 4:36 PM, James Kress <jimkress_58_at_kressworks.org>
wrote:

> Rst7 files generated by Amber cpptraj are not readable by VMD 1.9.3 I
> found
> the following in the mailing list. Has this bug been fixed yet? I am
> using
> VMD 1.9.3 on Win7 Pro and RHEL Linux. Both suffer from this issue.
>
> Thanks for any assistance.
>
> Jim Kress
>
> VMD-L Mailing List
>
> From: John Stone (johns_at_ks.uiuc.edu)
> Date: Fri Feb 03 2017 - 00:18:05 CST
>
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> In reply to: Vlad Cojocaru: "reading rst7 files generated by cpptraj"
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>
> Vlad,
> If you can send me some gzipped example files that have this formatting,
> I can take a crack at it when I get a chance.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Jan 27, 2017 at 11:28:30AM +0100, Vlad Cojocaru wrote:
> > Dear VMD users,
> >
> > I noticed that VMD cannot properly read the rst7 created by CPPTRAJ. The
> > reason for this appears to be the formatting of the second line (see
> > below). The number "0.0000000E+00" represents the time in "ps". Removing
> > it makes the file readable by VMD with the rst7 file format.
> >
> >
> > *** first 2 lines of rst7 file created by CPPTRAJ ***
> > Cpptraj Generated Restart
> > 226253 0.0000000E+00
> >
> > It could be nice if the plugin could be modified to read these files
> > correctly.
> >
> > Best wishes
> > Vlad
> >
> >
> >
> > --
> > Vlad Cojocaru, Ph.D., Project Group Leader
> > Department of Cell and Developmental Biology
> > Max Planck Institute for Molecular Biomedicine
> > Röntgenstrasse 20, 48149 Münster, Germany
> > Tel: +49-251-70365-324; Fax: +49-251-70365-399
> > Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>
>
>