Thank you for your reply.
To analyse trajectories using cpptraj, .prmtop files are a requirement. So,
how can I combine various trajectories that were generated from different
prmtop files?
Is it possible to strip the .prmtop to contain only the peptide information
and then load all stripped trajectories ?
On Mon 14 May, 2018, 2:09 PM David A Case, <david.case.rutgers.edu> wrote:
> On Mon, May 14, 2018, Chetna Tyagi wrote:
> >
> > I have carried out different simulations of the same peptide with
> classical
> > MD and accelerated MD. The parameter files that I used for these were
> > different.
> >
> > Similarly, in chloroform solvent, I have used two different parameter
> files
> > for some reason.
> >
> > Is it possible to strip the solvent from parameter files and combine
> these
> > trajectories to analyze only the peptide and project it on the same PCA
> > landscape?
>
> Yes: PCA analysis doesn't depend on the force field parameters which
> were used in the underlying trajectory: it just analyzes the
> fluctuations in coordinates. So, if all the stripped trajectories have
> the same number of atoms (in the same order), you should be fine.
>
> Of course, if the force fields differ in significant ways, it may be
> difficult to interpret the results you obtain.
>
> ....dac
>
>
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Received on Mon May 14 2018 - 05:30:04 PDT
