[gmx-users] Yet another question about what force field to use

Justin Lemkul jalemkul at vt.edu
Wed Aug 14 15:43:36 CEST 2013

On 8/13/13 10:26 PM, Pedro Lacerda wrote:
> Hi all,
> Many questions about how to choose a force field are addressed to this
> list, sorry if this one was already answered.
> Some argue that proteins are better modeled with ff99sb-ildn or charmm22*
> because occur great agreement between NMR experiments and simulations when
> using these force fields. But what about organic heteromolecules? One could
> say that organic molecules are similar enough to amino acid side chains
> concluding that protein force fields are adequate to model these molecules,
> but I'm not sure.
> What ff would best describe a small ligand bound to protein? What do you
> think?

I don't think this question can be asked in the absence of the underlying choice 
of the protein force field.  The ligand parameters are only as good as the 
results of the parameterization of it, within the context of the parent force 
field's criteria.  All force fields can be extended to describe new species, 
though the methods to do so vary.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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