VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 17 2011 - 11:03:29 CDT

David,
  Just a quick note regarding the new CHARMM PSF files:
So long as they are marked with the EXT tag, I expect that the VMD
PSF reader plugin should "do the right" thing now. If we find
any cases where it does not, they should be relatively easy to fix.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 12, 2011 at 09:51:39PM +0000, David A. Horita wrote:
> 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
> 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> 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 

-- 
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