From: Hannes Loeffler (Hannes.Loeffler_at_stfc.ac.uk)
Date: Thu May 28 2015 - 13:19:14 CDT
Many thanks. But I think it goes without question that there needs to
be internal consistency between the files.
Anyway, I have looked through the source of c38b1 and the character
lenghts of atom types are A4 in the traditional format and A6 in the
extended format. The data type is CHARACTER which I would expect to be
ASCII but maybe there are differences with different compilers. In any
case, this should, in principal at least, give a wide range of possible
On Fri, 22 May 2015 09:55:44 -0500
Josh Vermaas <vermaas2_at_illinois.edu> wrote:
> 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
> (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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