VMD-L Mailing List

From: David A. Horita (dhorita_at_wfubmc.edu)
Date: Thu May 12 2011 - 16:51:39 CDT

I ran into this problem in 2008 with some modified CHARMM files - 4 characters works for atom names from a VMD perspective, but the newer charmm rules allow up to 8 characters. The CG2R51 is causing the problem. It's the A8, not the G14.6.

John might be able to dig out some communication with me and Alex MacKerell about this from 2008-

CHARMM is currently being modified to accept 8 characters, which will be the standard into the future. That's why I've gotten in touch with you to insure that NAMD/VMD can handle 8 characters. Youngdo Won and Bernie Brooks are the ones doing the modification. I'm ccing this to them so they can comment if necessary.

thanks, alex

John Stone wrote:
> Hi,
> I think the root of the problem here is that the CHARMM PSF format
> uses integer indices for the atom type field, and psfgen and NAMD use
> the X-PLOR scheme of using that field as an atom type string.
> The CHARMM PSF formats only allow 4 characters for the atom type,
> which is fine if you use an integer index as they use in their Fortran
> format string, but that's insufficient for the actual atom type
> string. The CHARMM EXTended PSF format is (if CMAP,CHEQ are also included):
> '(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,I4,1X,2G14.6,I8,2G14.6)'
>
> The PSF file you sent illustrates this problem clearly.
> Note that the columns are shifting, which should never occur given
> that all existing variants of the PSF format uses fixed field widths:
> 24 !NATOM
> 1 O1 124 INI1 C1 CC3161 0.140000 12.0110 0
> 2 O1 124 INI1 H1 HCA1 0.090000 1.0080 0
> 3 O1 124 INI1 O1 OC311 -0.650000 15.9994 0
> 4 O1 124 INI1 HO1 HCP1 0.420000 1.0080 0
> 5 O1 124 INI1 C5 CC3161 0.140000 12.0110 0
> 6 O1 124 INI1 H5 HCA1 0.090000 1.0080 0
>
> There's no existing PSF variant that I'm aware of that will accept
> more than 4 characters for the atom type info, so we will either need
> to create a NAMD-specific variation that eliminates these fixed field
> width issues entirely, or adopt a new file format instead of
> continuing to (ab)use the PSF format.
>

Regards,

David
-----------------------------
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016
Tel: 336 713-4194
Fax: 336 716-7671
email: dhorita_at_wfubmc.edu<mailto:dhorita_at_wfubmc.edu>
web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm>

________________________________
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Grant Schauer
Sent: Thursday, May 12, 2011 3:16 PM
To: John Stone; Axel Kohlmeyer; Grant Schauer; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Large positive non-integer charge

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<mailto: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<mailto: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<mailto: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<mailto:akohlmey_at_gmail.com> http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA. 

--
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