AMBER Archive (2000)

Subject: coordinate averaging

From: Prem Raj Joseph (prbj_at_hotmail.com)
Date: Thu Jun 29 2000 - 17:18:13 CDT

Hi ,

I have a problem while doing coordinate averaging using carnal . I use the
below input

#Simple Coordinate Averaging
FILES_IN
  PARM p1 bdna25n.top;
  STREAM s1 bdna25_1.imaged.Z;
FILES_OUT
  COORD c1 ave.pdb PDB;
DECLARE

OUTPUT
  COORD c1 s1 AVERAGE;
END

If I give the original trajectory file ( without imaging ) as input ( under
the card STREAM). I get a output average PDB file ie ave.pdb. But if I use
the imaged trajectory file, carnal does run without any error, but there is
no output PDB file created. What could be the problem. Also If I give a
number of trajectory files as input, the program reads ony the first one.

Secondly how should I modify the above input for coordinate averaging the
solute alone ( without water)as well as only the molecule. If I specify a
group under Declare card , where should I include the group ID in the OUTPUT
card.

Thanks in advance.

Prem raj

#############################################
Prem Raj B.J.
Dept. of Crystallography and Biophysics
University of Madras
Guindy Campus
Chennai 600 025
email : prbj_at_hotmail.com , prbj_at_joymail.com
phone : 4353229 (residence) , 2351367 (Dept)
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