VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Jul 29 2013 - 12:35:01 CDT

Just add NAMD to the top line of a psf file:

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.
-Josh

On 07/29/2013 10:47 AM, Thomas Albers wrote:
> Hello!
>
>> This has been discussed a few times in this list (I asked the same question about a year ago). Basically, the problem is that the long atom types break the rules of the original PDB standard, which is based on strict field lengths.
> Thanks, I found that message now. Over there in that thread John says
> that the issue has been addressed in the development version. What's
> with this NAMD flag that tells VMD that it is dealing with a
> non-standard psf file? What's its syntax so I can edit it into the
> psf file once I have compiled VMD 1.9.2 alpha?
>
> Regards,
> Thomas