VMD-L Mailing List

From: Grant Schauer (grantschauer_at_gmail.com)
Date: Thu May 12 2011 - 18:03:12 CDT

"4 characters works for atom names from a VMD perspective, but the newer
charmm rules allow up to 8 characters."

Yes, I was going to mention that NAMD had no problem handling the same PSF.
Oh well, manually defining the number of ions is about the easiest
workaround I could ask for... thanks everyone!

Grant

On Thu, May 12, 2011 at 5:51 PM, David A. Horita <dhorita_at_wfubmc.edu> 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
>>
>
>