VMD-L Mailing List

From: James Kress (jimkress_58_at_kressworks.org)
Date: Thu May 17 2018 - 21:24:15 CDT

Robin,

 

Thanks!

 

Jim

 

 

From: robinmbetz_at_gmail.com <robinmbetz_at_gmail.com> On Behalf Of Robin Betz
Sent: Thursday, May 17, 2018 8:45 PM
To: jimkress_58_at_kressworks.org
Cc: John Stone <johns_at_ks.uiuc.edu>; Vmd l <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: rst7 as input file bug

 

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 <mailto: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 <http://johns_at_ks.uiuc.edu> )
Date: Fri Feb 03 2017 - 00:18:05 CST

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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 <http://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 <http://mpi-muenster.mpg.de>