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?
> >
>
> No, 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
