[gmx-users] CHARMM nonbonded parameters and grompp output
Mark.Abraham at anu.edu.au
Fri Feb 22 01:56:04 CET 2008
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 :-)
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