VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 07 2013 - 13:48:21 CDT

Hi guys,
  The newest test builds of VMD 1.9.2 have a new psfgen that
Jim made that knows about the NAMD flag etc. We are testing it
internally currently, but I expect it to be posted in the biocore
test area soon so that others can try it as well.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jul 29, 2013 at 04:22:49PM -0400, Thomas Albers wrote:
> Hello!
>
> > PSF NAMD
> >
> > It makes VMD read in the psf file the same way NAMD does, reading in the
> > columns in a space-delimited way. Compiling 1.9.2 may not be needed
> > either. I believe (although am by no means certain), that the NAMD flag
> > is also respected in 1.9.1.
>
> I can confirm that VMD 1.9.1 respects the NAMD flag. Thanks for the hint!
>
> It would be a good thing, though, if psfgen knew about the NAMD flag
> and set it if necessary. psfgen 1.6 reads in topologies and PSF files
> with long atom types correctly and writes out a NAMD-type PSF. It
> would be great if it set the NAMD flag automatically if it has to spit
> out a non-standard psf file. The fact that it doesn't to it almost
> qualifies as a bug.
>
> Thanks,
> Thomas 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/