Re: [AMBER] cpptraj script for average 3D protein structure?

From: Repic Matej <matej.repic.epfl.ch>
Date: Thu, 10 Sep 2015 09:58:59 +0000

I think adding another line after the trajin 3_ would do the trick:

trajin ../4_/sm_md4.mdcrd 2000 4000


Best,
Matej

------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ­ LCBC
BCH 4108
CH - 1015 Lausanne
------------------------------------------------------







On 9/10/15, 10:23, "Michael Shokhen" <michael.shokhen.biu.ac.il> wrote:

>Dear Amber List users,
>
>
>I now how write a cpptraj script for the generation of average protein
>structure from
>
>MD simulation in one directory as for instance:
>
>
>cpptraj
>parm ../sm.prmtop
>trajin ../3_/sm_md3.mdcrd 1001 2000
>strip :WAT
>strip :Cl-
>rms first .C,CA,N
>average average.pdb PDB
>run
>
>
>Unfortunately, I don't know how to write a cpptraj script for time
>interval
>
>that covers the border between two sequential directories of continuous
>MD simulation like in the task described below.
>
>
>I have ran productive MD simulation of my protein
>
>in two sequential time intervals 20ns (2000 snapshots) in directory 3_,
>
>and then continuing simulation of 20ns (2000 snapshots) in directory 4_.
>
>As a result I have in total 40ns (4000 snapshots) MD simulation.
>
>I want to generate average 3D structure of my protein on the last 30 ns
>
>(3000 snapshots) time interval that includes a border between two
>sequential MD simulations.
>
>
>What should be a cpptraj script for this case?
>
>
>Thank you,
>
>Michael
>
>
>
>
>*****************************
>Michael Shokhen, PhD
>Associate Professor
>Department of Chemistry
>Bar Ilan University,
>Ramat Gan, 52900
>Israel
>email:
>shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b
>9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
>_______________________________________________
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>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber


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Received on Thu Sep 10 2015 - 03:00:03 PDT
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