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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Received on Thu Jun 23 2011 - 06:00:04 PDT
