VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Mon Aug 19 2013 - 19:53:11 CDT

Hi Josh,

Thanks for this tip. Just a note: with the latest build of VMD 1.9.2 (a29), autoionize correctly calculates charge at the beginning and adds the correct number of ions. However, the output psf is written with PSF CMAP in the header, leading it to calculate a nonsensical charge:

Autoionize) System net charge after adding ions: 2402.2600336149335e

and throw up a warning. Harmless problem, as long as one knows about it - and will of course be fixed by your upcoming update to psfgen.

Cheers,

Tristan

-----Original Message-----
From: Josh Vermaas [mailto:vermaas2_at_illinois.edu]
Sent: Tuesday, 30 July 2013 3:35 AM
To: Thomas Albers
Cc: Tristan Croll; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Problem with autoionize plugin and long atomtypes

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