From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri May 22 2015 - 09:55:44 CDT
Hi Hannes,
It depends. The original psf specification was developed for CHARMM, and
originally each of the fields was allowed to be only 4 characters long
(this was a decision made a long time ago, so it seemed reasonable at
the time). However, around the time CGenFF and the sugar force fields
were being expanded, it became apparent that 4 characters wasn't going
to cut it anymore, as it was really convenient to have the first
character of an atomtype indicate the element. CHARMM introduced an
extended format to deal with the explosion of atomtypes, which double
the length of each field to 8 characters
(http://www.charmm.org/documentation/c39b1/io.html#%20IOFORM). VMD and
NAMD will handle either one just fine, but as Aaron mentioned, the most
important thing is to be consistent, and have distinct atomtypes have
unique names. Check existing CHARMM36 force field files for the
atomtype. If it exists, consider giving your new atomtype a different name.
-Josh Vermaas
On 05/22/2015 07:34 AM, Aaron Larsen wrote:
> Hi Hannes,
>
> I've had success with custom names for atom types, but I haven't tried
> anything longer than 4 characters. The most important thing seems to
> be consistency. As in, the atom type names in the topology file, the
> parameter file, and the psf file must all match up. Failure to remain
> consistent results in errors.
>
> Best,
> Aaron
>
> On Fri, May 22, 2015 at 5:42 AM, Hannes Loeffler
> <Hannes.Loeffler_at_stfc.ac.uk <mailto:Hannes.Loeffler_at_stfc.ac.uk>> wrote:
>
> Hi,
>
> I was wondering what constraints there are on the naming of the
> atom types in those files. The longest I have seen so far is four
> characters long. Is that the limit? Are they case-sensitive? What
> character set do they draw from? Any special rules for first
> character? etc.
>
> Many thanks,
> Hannes.
>
>
>
>
> --
> Aaron Larsen, Ph.D.
> Harvard University Department of Chemistry and Chemical Biology
> Harvard Medical School Department of Genetics
> E-mail: alarsen_at_molbio.mgh.harvard.edu
> <mailto:alarsen_at_molbio.mgh.harvard.edu>
> Mobile: 617-319-3782
> FAX: 617-643-3328
>
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