Jacopo many thanks for the advice and the references, these papers are
exactly what I was looking for!
Prof Case I was actually looking at section "6.3 Chemical shift restraints"
of Amber11 manual before posting. Perhaps it applies only to NMR structure
refinement with SA (hence the title of the chapter is " NMR and X-ray
reļ¬nement using SANDER") and not conventional MD, but even in that case the
chemical shifts could be useful to generate initial conformations in the ID
state. There is a crystal structure of the peptide bound to its partner
where it assumes an alpha-helical form, and I am currently setting up a REMD
simulation to unfold it (the monomer assumes an ID state). Unless I am
missing something (probably yes), it would be helpful to clarify in the
manual what kind of chemical shifts can be utilized as restraints and for
what purpose.
Thomas
On 23 June 2011 15:58, DEBOSTUTI GHOSHDASTIDAR <debostutighosh.gmail.com>wrote:
> Hi Prof David
>
> I have been running a simulation of a peptide for sometime now which
> according to CD studies is a random coil. I am allowing ff99SB to do its
> job
> and the peptide is rapidly shifting from alpha to pi to short beta....just
> thought will tell you about it...dunno if this will help
>
> Debostuti
>
> On Thu, Jun 23, 2011 at 5:52 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
>
> > On Thu, Jun 23, 2011, Thomas Evangelidis wrote:
> > >
> > > I want to simulate the dynamics of an *intrinsically disordered
> *peptide
> > (40
> > > aa) at 298 K and 1 bar, with ff9SB-ILDN or ff99SBnmr1. I have 13CO,
> 13Ca,
> > > and 13Cb NMR chemical shift values for a homologous peptide (82%
> sequence
> > > identity, 90% sequence similarity) which all lie within the random coil
> > > area. Do you reckon it is worth applying chemical shift restraints
> taken
> > > from the homologue to my target peptide , or just leave the ff do its
> job
> > > and then see if the calculated chemical shifts correlate with the
> > > experimental? I would greatly appreciate any comments about this case.
> >
> > Amber doesn't have any code to apply C', Ca and Cb restraints, disordered
> > or
> > not. Nor is there any simple way to force the simulation to have a
> certain
> > region be disordered (say as a time average). The option to "leave the
> ff
> > to
> > do its job" is about the only option I can think of, at least for the
> > current
> > Amber codes.
> >
> > ...dac
> >
> >
> > _______________________________________________
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> >
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>
--
======================================================================
Thomas Evangelidis
PhD student
Biomedical Research Foundation, Academy of Athens
4 Soranou Ephessiou , 115 27 Athens, Greece
email: tevang.bioacademy.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Jun 23 2011 - 09:30:06 PDT
