AMBER Archive (2003)

Subject: RE: AMBER: CARNAL

From: Ming Lei (MILei_at_clarku.edu)
Date: Mon Aug 25 2003 - 14:27:42 CDT

Hi, Wen:

Why not have a try? I just tested SELECT option to get the average
structure for the first 400 snapshots in a 1200 snapshots trajectory.
It worked well.

Wish it could help.

Ming

-----Original Message-----
From: Wen Li [mailto:liw_at_wadsworth.org]
Sent: Monday, August 25, 2003 10:30 AM
To: amber_at_scripps.edu
Subject: AMBER: CARNAL

Dear AMBER-users,

I am trying to get an average structure from snapshots 1-500 of
an MD trajectory which includes a total of 1000 snapshots. Could anyone
tell me how to change the following batch file for CARNAL that is for
generating an average for the total 1000 snapshots? Do I have to use
SELECT to obtain the 500 snapshots first? Thanks!

FILES_IN
  PARM p1 topo;
  STREAM s1 md.traj;
  STATIC refset md.rst;
  
FILES_OUT
 COORD crd average.pdb PDB;

DECLARE
  GROUP grp1 (RES 1-50);
  RMS fit1 FIT grp1 s1 refset;

OUTPUT
 COORD crd fit1 AVERAGE;
 
END

Wen

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