[gmx-developers] Re: Amber to Gromacs forcefield conversion

B.Hess at chem.rug.nl B.Hess at chem.rug.nl
Thu May 23 10:27:24 CEST 2002

> >
> >As you say, the impropers aren't right yet - the angle and force constant
> >are the wrong way round. More worryingly, these are just the impropers for
> >pi-bonding: the impropers that maintain the geometry of chiral centres are
> >missing, and I can't see them in the amber force field files either - are
> >they generated automatically by amber? Maybe we should just generate one
> >for every sp3-hybridized atom (...that doesn't have two or three hydrogens
> >on it)? 
> >
> I don't think you need them with the all-atom force field. At least 
> that's the case with OPLS-aa;
> since we explicitly include all four atoms around the chiral centers the 
> geometry won't distort.
> (The energy barrier for L-R conversions is just as high as it is in nature!)
> OPLS-aa might be slightly different in that it includes all proper 
> dihedrals, though.

This is not really a question of needing.
If they are in the original forcefield they should also be in Gromacs
as they do influence the potential.
You are right that the chirality probably would not change during a simulation.
But in some cases you really want to have right. Especially when comparing
with NMR data it is important that the chirality is correct, also of CH3 and
NH3 groups. Some pdb files contain incorrect chirality, which is very hard
to find out without impropers.
Nasty problems can also occur with chirality of sidechains like ILE which,
if I remember correclty, do not follow the IUPAB rules in the official
gromos forcefield.


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