[gmx-users] CHARMM nonbonded parameters and grompp output

[Mark Abraham]

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 :-)

Mark