AMBER Archive (2004)

Subject: Re: AMBER: ptraj & LES

From: Michael Trieb (Michael.Trieb_at_uibk.ac.at)
Date: Mon Feb 02 2004 - 11:11:08 CST

Dear Vlad,

I am quite sure that it is also possible with ptraj, but for me CARNAL
worked (and I think in both cases you have to specify the atoms
belonging to each copy...and that's the time consuming part).
In my case I had DNA and a ligand, and part of the ligand I defined as
my LES region
Here a sample file:

FILES_IN
  PARM p1 prmtop;
  STREAM s1 *.mdcrd;
FILES_OUT
  COORD c1 name1.crd CRD;
  COORD c2 name2.crd CRD;
  COORD c3 name3.crd CRD; ...
DECLARE
  GROUP g1 (ATOM 1-890, 1091-1118, 1319-1338); #DNA
  GROUP g2 (ATOM 891,896,901,906,911,916,921,926,931,936,941,....);
#every 5th atom of LES region 1st copy
  GROUP g3 (ATOM.......); #every 5th atom of LES region 2nd copy...
  GROUP g12 ((GROUP g1) | (GROUP g2)); #DNA+1st copy
 GROUP g13 ((GROUP g1) | (GROUP g3)); # DNA+2nd copy
OUTPUT
  COORD c1 GROUP g12;
 COORD c2 GROUP g13;........
END

Hopefully you don't have too many copies....

Michael

Vlad Cojocaru wrote:

> Dear Amber users,
> I read a message (a while ago) that ptraj can separate the LES
> trajectory into separate trajs for each copy. Has anyone ever done that?
> Best wishes
> vlad
> 

-- 
Michael Trieb
University of Innsbruck
Institute of General, Inorganic
and Theoretical Chemistry
Innrain 52a
A-6020 Innsbruck
e-mail: michael.trieb_at_uibk.ac.at
Tel.: +43(0)512/507-5142

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