VMD-L Mailing List

From: Grant Schauer (grantschauer_at_gmail.com)
Date: Thu May 12 2011 - 14:16:14 CDT

Hi John,

Yes, that must be it. Large atom names from CGenFF appear to be pushing
charges over, e.g.

35 O1 4 RES CL10 CS -0.040000 12.0110
0
36 O1 4 RES CL11 CG2R51 -0.160000 12.0110 0

It would be easy enough to correct by hand, if I can fit the atom name in
the column. Do you happen to know the required column widths or could you
point me to the PSF documention? From this post

http://www.charmm.org/ubbthreads-7-5-3/ubbthreads.php?ubb=showflat&Number=12687

it looks like "G14.6" but I don't know how to interpret that...

Thanks for your help
Grant

On Thu, May 12, 2011 at 3:00 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Grant,
> I suspect it is likely that the PSF might be misformatted, and
> that one of the values is going outside of the fixed-width fields.
> Please send me a gzipped copy of the PSF file and I'll gladly have a look.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, May 12, 2011 at 02:56:44PM -0400, Axel Kohlmeyer wrote:
> > On Thu, May 12, 2011 at 2:16 PM, Grant Schauer <grantschauer_at_gmail.com>
> wrote:
> > > Hello all,
> > >
> > > I'm trying to solvate a small system consisting of a small peptide
> patched
> > > to a novel residue built from CGenFF definitions. When I attempt to
> > > autoionize the system after solvating, I get a warning that I have a
> > > non-integer charge. In fact, it's measuring +67.08000009506941e.
> > >
> > > I get the same number with the following commands (regardless of
> whether
> > > it's solvated):
> > >
> > > set sel [atomselect top all]
> > > set charge [vecsum [$sel get charge]]
> > >
> > > But when I add up the charges from the PSF by hand, I get exactly the
> > > integer (+2) that I expect, as specified in my topology file. Autopsf
> runs
> > > smoothly, with no complaints that I'm seeing. I'm running VMD 1.9.
> > >
> > > Any suggestions? Thanks,
> >
> > VMD uses single precision floating point numbers,
> > which have only about 7 valid digits in the mantissa.
> > for a system with a large enough number of charged
> > atoms, this kind of non-integer rest may be the consequence
> > of simple rounding and truncation errors.
> >
> > axel.
> >
> >
> > > Grant
> > >
> > >
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer
> > akohlmey_at_gmail.com http://goo.gl/1wk0
> >
> > Institute for Computational Molecular Science
> > Temple University, Philadelphia PA, USA.
>
> --
> NIH Resource 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/ Fax: 217-244-6078
>