[gmx-users] CHARMM nonbonded parameters and grompp output

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 22 02:05:58 CET 2008

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

> Justin A. Lemkul wrote:
> > Thanks for the detailed and informative reply, Mark (as always).  I have
> decided
> > there is probably something fundamentally wrong with what I've been doing.
> I've
> > been at this for several months, every time I get a few free minutes from
> my
> > main work, so I lost track of what I did at the very beginning (oops).  I
> tried
> > to start from scratch, using your scripts to get ffcharmmbon.itp and
> > ffcharmmnb.itp, since I know I have tried different iterations of your
> scripts
> > and the awk scripts.
> >
> > When I tried to start from scratch using your convert_charmm_to_gromacs.pl
> on
> > the CHARMM .prm file, but it exited with this:
> >
> > Sin of delta not zero, hope this is the only dihedral of
> >  type     X    CS    SS     X
> >  (sin delta = 0.00349065141522373)
> It doesn't exit with that message, that's a warning along the way.
> CHARMM needs to define multiple periodic dihedrals for the same atoms,
> and GROMACS is not able to use a sum of multiple copies of its periodic
> dihedrals for the same set of atoms. To compromise, you convert them to
> R-B form. This works so long as you don't need periodicity >= 6, and so
> long as the angle offset (delta above) has sin(delta) = 0 if there are
> actually more than one.
> If sin(delta) != 0, then the script leaves it in periodic form and use
> the above warning to alert the user... if there's more than one such
> dihedral for a set of atom types, then you'll get more than one such
> message and can be clued into the problem.
> > 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.

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.

The input to the script was par_all27_prot_lipid.prm (that might be important
information that I also failed to mention before).


> 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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