Re: [AMBER] Converting (rst) file to PDB using ambpdb

From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
Date: Wed, 6 Aug 2014 10:48:25 +0200

Whenever there .rst extension it is the last file.

Now I think you are most interested in md average structure. Use this scipt

reference Full_Mini.rst

trajin strip.bps

trajout almin.bps binpos nobox

rms reference out rms-min.dat @CA

average av.pdb * pdb nobox


To get the possible stable structure is not the average structure. Check
the CA backbone fluctuation of a system. Say for example you got a starting
structure and you saw that after 20ns it is quite stable till the end.


Then take snapshot corresponding PDBs with an interval and superimpose it
to check if the parameters are reasonable in all case or not.


To take snapshots use this


trajin md.mdcrd

outtraj snapshot30.pdb onlyframes 30000 (this will dump a PDB named
snapshot30.pdb which will correspond to 30000)


Use CPPTRAJ to execute


On Wed, Aug 6, 2014 at 12:18 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:

> In particular, the 'rst' file represents the end coordinates and
> velocities for the run.
>
> Bill
>
> <div>-------- Original message --------</div><div>From: Jason Swails <
> jason.swails.gmail.com> </div><div>Date:08/05/2014 2:57 PM (GMT-08:00)
> </div><div>To: menwer momo <masalmeh2007.yahoo.com>, AMBER Mailing List <
> amber.ambermd.org> </div><div>Subject: Re: [AMBER] Converting (rst) file
> to PDB using ambpdb </div><div>
> </div>On Tue, Aug 5, 2014 at 4:40 PM, menwer momo <masalmeh2007.yahoo.com>
> wrote:
>
> > Hi,
> >
> > One can convert the coords file (rst) of a "production" simulation to a
> > PDB file to take a look at the structure. Does this structure represent
> the
> > most stable structure obtained in that simulation or what?
> >
>
> ‚ÄčNo, it's just a structure in the ensemble like any other.
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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-- 
Thanks & Regards;
Soumendranath Bhakat
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Received on Wed Aug 06 2014 - 02:00:02 PDT
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