[gmx-users] CHARMM nonbonded parameters and grompp output

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 22 03:30:31 CET 2008

Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:

> Justin A. Lemkul wrote:
> >>> The ffcharmmnb.itp file is incomplete, and I suspect ffcharmmbon.itp is
> as
> >> well.
> >>>  Any idea what's going on?
> >> No, since you haven't said why you think they're incomplete :-)
> >
> > Sorry, I sent that a bit too quickly, didn't I?  I suspect ffcharmmnb.itp
> is
> > incomplete because it contains only 40 lines, with C as the first entry and
> HT
> > as the last entry.  There are no entries for any atom types other than
> carbon
> > and hydrogen.
> Right, well that is far too short. HT should not even be the final H
> atom-type. The code writes all of the [atomtypes] in the same foreach
> loop, which is just dumping pre-constructed lines of text. The fact that
> this has only written 40 of many more lines suggests the problem is
> external to the script. Full file-system? Killed process? Try again?

Yep, this one is a real stumper.  My filesystem has 11.5 GB available on the
partition I'm trying to write to, and I've tried a couple more times, using a
fresh download of your scripts (just to be sure, even though I'm sure I haven't
changed it).  I know I haven't modified the .prm file in any way, and the
process doesn't seem to be getting killed.

Perl version is 5.8.6 on Mac OS X 10.4.11, although I get the same output on an
Ubuntu Linux machine running Perl 5.8.8.  I don't know if that makes any
difference, although I doubt it should.

Is there anything I can do to diagnose this issue?  Sorry to say I'm not fluent
in Perl :-(



> > Perhaps ffcharmmbon.itp is alright - 1364 lines - entries for bonds,
> angles,
> > Urey-Bradley potentials, dihedrals, and impropers.  I just assumed
> something
> > had gone wrong because as soon as I got the message I mentioned, the script
> > stopped running.
> Yes that file is fine - it gets written before the other.
> > The input to the script was par_all27_prot_lipid.prm (that might be
> important
> > information that I also failed to mention before).
> Useful information. This is the version I designed the method using, so
> it ought to work perfectly, unless the above file has been modified :-)
> Mark
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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