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.wadsworth.org]
Sent: Monday, August 25, 2003 10:30 AM
To: amber.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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Received on Mon Aug 25 2003 - 20:53:01 PDT
