AMBER Archive (2009)

Subject: Re: [AMBER] Nonstandard molecules simulated with parm99EP ?

From: Marek Maly (
Date: Wed Jul 01 2009 - 11:02:29 CDT

Dear prof. Case,

thank you very much for your response especially for that special
antechamber flag to get parm99 like atom types in PREPINs. If am not wrong
I can use the same flag
for parm99EP since they have the same atom types labels ( except lone



Dne Tue, 30 Jun 2009 18:19:00 +0200 case <>

> On Tue, Jun 30, 2009, FyD wrote:
>> >"How it is possible to force the antechamber to use some different
>> >forcefield from GAFF ( like for example parm99EP
>> >for parametrisation of the relevant residui (generating of
>> >PREPIN/FRCMOD files) ?"
> This is not possible in general. You can use the "-at amber" flag to
> get parm99 atom types assigned, but that won't work well for arbitrary
> molecules, since many common ligand environments are not present in
> proteins and nucleic acids.
>> Personnally, I always use parm99 FF atom types for organic
>> molecules/protein/nucleic acid and add FF atom types manually; pick up
>> only _classical_ force field parameters from GAFF (bond & angle force
>> constants, aromatic dihedrals) and adapt them to parm99 way. Get
>> equilibrium values from high ab initio geometry optimization or X-ray
>> structures (not from GAFF). Key dihedrals are always refitted (not
>> obtained from GAFF).
>> What you said above summarize exactly the problem "so some inacuracy
>> regarding to specific molecules is "penalty" for it's
>> transferability/universality". When you use GAFF automatically all is
>> fine if your molecule has been well parametrized but you do not know
>> if it was indeed well parametrized...
> I want to second Francois' comments here: The gaff parameters can be
> considered as an (often good) starting point for molecular mechanics
> parameterization, but the procedure outlined above should generally give
> better results -- especially the advice about refitting key dihedrals.
> Be especially critical of gaff recommendations where your ligand has
> extensive
> conjugation or bonds with partial double-bond character. On the other
> hand,
> gaff should be pretty good for saturated compounds (like, say, fatty
> acids or
> many lipids), or where you have "simple" aromatic groups where it is
> easy for
> antechamber to assess the extent of electron delocalization.
> Of course, for projects like virtual screening of large databases, one
> must
> generally accept the compromises inherent in gaff, since it is not
> feasible to
> perform hand-optimization on thousands of ligands.
> ...dac
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