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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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