just to add a bit to what Dave said, make sure you think about protonation
states for your peptides in the gas phase. The defaults may not be
appropriate, so just check.
On Thu, Mar 24, 2016 at 12:46 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Thu, Mar 24, 2016, Edwin Aponte wrote:
>
> >
> > We want to predict peptide structures in vacuum, to calculate their
> > collision cross sections and compare them with ion mobility spectrometry
> > results. We want to use polarizable force fields and compare with ff14SB.
> >
> > Is it right to use ff14ipq in vacuum? Do you know any other polarizable
> > force field that could be used in vacuum?
>
> In the upcoming release of AmberTools16, we will have a learpc.ff15ipq_vac
> file, which uses vacuum charges, and which was fit against vacuum quantum
> energies. This is the closest thing Amber has to a vacuum force field for
> peptides: note that (as Carlos pointed out) it is not a polarizable force
> field, and has not been tested very much (or at all) on real peptides in
> the
> gas phase.
>
> ....dac
>
>
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Received on Thu Mar 24 2016 - 10:30:03 PDT
