Hi Vishal,
There are a variety of aspects about your specific
problem/question/hypothesis you will need to consider carefully. Choosing a
force field that is appropriate for your problem/question/hypothesis is
very important; as such, it might be helpful to dive even further into the
literature. If you haven't already done so, please take a look at some
recent articles from the Amber clan (there are other clans; for brevity's
sake below I list just a tiny fraction of Amber's force field papers):
AmberMD.org -- please leverage the information provided on this page!
http://ambermd.org/#ff
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone
Parameters from ff99SB
http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00255
Folding Simulations for Proteins with Diverse Topologies Are Accessible in
Days with a Physics-Based Force Field and Implicit Solvent
http://pubs.acs.org/doi/abs/10.1021/ja5032776
ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of
Proteins
http://pubs.acs.org/doi/abs/10.1021/ct500643c
Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for
Noncovalent Interactions
http://pubs.acs.org/doi/abs/10.1021/ct500799g
Are you trying to compare the stability of your peptide in different
environments (e.g. different dielectrics, like gas phase, water, buffer con
ions, lipid layers)? Are you trying to fold a sequence from scratch? Are
you trying to compare subtle dynamics such as side chain packing? Are you
trying to model large domain motions? Given an experimental structure, are
you trying to compare the relative stability of different 42 residue
sequences? And so on; your question needs focusing, because our answers
here on the Amber list will depend entirely on the specific of your
problem/question/hypothesis.
HTH,
K
On Wed, May 25, 2016 at 8:41 AM, Vishal Nemaysh <
vishal.bioinfotech.gmail.com> wrote:
> Respected Carlos Sir i want to simulate a peptide of 42 amino acid
> residues, and for this purpose i want to know, which force field is
> suitable.
>
> On Wed, May 25, 2016 at 5:21 PM, Dr. Anselm Horn <anselm.horn.fau.de>
> wrote:
>
> > Hello,
> >
> > in case your peptide system has already been investigated via MD
> > similations, you may want to have a look into the literature. Perhaps,
> > there are publications around that made used of an Amber force field,
> > and thus you had something to start and compare with.
> > (Especially, if your peptide was amyloid beta, which would fit the
> > particular number of residues, there is a multitude of articles
> available.)
> >
> > Regards,
> >
> > Anselm
> >
> > Am 25.05.2016 13:22, schrieb Vishal Nemaysh:
> > > Hello all,
> > >
> > > I want to know about what kind of Force Field utility used
> > for
> > > a peptide simulation, which possess only 42 amino acid residues. please
> > > kindly let me know.
> > >
> > > Thanking you in advance
> > >
> > > Regards...
> > >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Vishal Nemaysh
> Research Scholar,
> Neuropharmaceutical Chemistry lab.,
> Dr. B. R. Ambedkar Center for Biomedical Research,
> University of Delhi, Delhi-110007
> Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
> Phone: 91-11-27662778 Mobile: 91+8447581401, 91+9650736653
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-- - -
HK
════════════════════════════════════════════
Kevin E. Hauser, Ph.D. Candidate
NRSA Fellow, National Institutes of Health
Carlos Simmerling Laboratory
Miguel Garcia-Diaz Laboratory
100 Laufer Center for Physical and Quantitative Biology
Stony Brook, New York 11794-5252
Phone: (631) 632.5394 Email: 84hauser.gmail.com
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Received on Wed May 25 2016 - 07:00:02 PDT
