Hi,
>Will I able to do PCA using Prody script following this strategy?
Amber trajectories can be processed by Prody but you have to change first the *.mdcrd trajectory file to dcd (charmm) before that.
Regards,
Filip
On Thursday, February 27, 2014 4:30 PM, Jason Swails <jason.swails.gmail.com> wrote:
On Thu, 2014-02-27 at 16:05 +0200, Soumendranath Bhakat wrote:
> Dear AMBER community;
>
> I have desmond trajectory and corresponding PDB which we used for MD using
> desmond integradted with Maestro. We want to chage it to amber trajectory.
Why? Nothing you propose to do uses any Amber programs.
> We found some useful script to change it to amber trajectory.
>
> I have two questions:
> 1. I want to upload desmond trajectory and corresponding PDB in VMD . Will
> I able to do PCA using Prody script following this strategy?
I have no idea. ProDy is not part of Amber (assuming you mean this:
http://prody.csb.pitt.edu/) and I've never used it before.
> 2. If I change desmond trajectory into amber, then upload amber mdcrd and
> corresponding pdb in VMD and then carry PCA using ProDy script. Will it be
> better than previous strategy?
No. VMD reads Desmond trajectories. Why convert it to an Amber
trajectory if you're just going to use VMD anyway?
Either this forum is the wrong place for your question or I completely
misunderstood what you're trying to do. Maybe see if prody has a place
you can ask questions (or, of course, you can just try things yourself
and see how it goes).
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 27 2014 - 07:30:03 PST
