On 8/12/13 8:19 AM, Maria Astón Serrano wrote:
Dear Gromacs users,
We would like to know which is the Force Field which is customarily
preferred for simulations of peptides and proteins.
Interestingly, this same question was just asked on the development list,
although the discussion indeed belongs here.
http://lists.gromacs.org/pipermail/gmx-developers/2013-August/007016.html
There is a wide body of literature on this topic, and it is very educational to
read through as much of it as you can. Some force fields, like AMBER94 and
CHARMM22+CMAP are decidedly too helical, while others (Gromos96 53A6 being a
good example) tend to understate helices and overstate extended configurations.
New parameter sets like AMBER99SB-ILDN and CHARMM22* are often used in protein
folding studies and seem to do quite well.
I think, in the end, it depends to some extent about the scope of what you are
doing and the protein(s) to be studied. Even high quality force fields that
perform well for folded proteins do not necessarily perform well on
intrinsically disordered proteins or model peptides.
-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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