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

Erik Lindahl lindahl at stanford.edu
Thu May 23 19:32:38 CEST 2002

B.Hess at chem.rug.nl wrote:

>>>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.
Of course - what I meant was that they aren't included in OPLS-aa for 
this reason, and I would guess they are not included in Amber either for 
the same reason :-)



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