Dear Amber users,
In Amber 5, when I try to create a coordinate-averaged PDB file for all or
part of an MD simulation, I get a structure with bond lengths that are
obviously wrong, causing rasmol or Insight to draw bonds between nonbonded
atoms. Parts of the structure (a DNA duplex solvated with a water box and
cations) are distorted. Here is a sample carnal input file:
FILES_IN
PARM p1 ../firstmdrun.top;
STREAM s1 ctr_last_5ns.mdcrd.gz; ! ptraj-processed crd file
FILES_OUT
COORD c1 prodmd5to10ns_avg.pdb PDB;
DECLARE
OUTPUT
COORD c1 s1 ATOM 656 AVERAGE; ! output only the DNA, no water/cio.
END
I realize that carnal is averaging the waters as well, and tried to
declare a group consisting of only the solute to avoid this, but the
program seemed not to recognize the declaration.
Is there a more recent version of carnal, analogous to the new ptraj
(6.3), that would work better for averaging?
Thanks very much for your help.
Sincerely,
Michael G. Cooney
Postdoctoral Research Associate
Department of Chemistry
Georgia State University
Atlanta, GA 30303, USA
Received on Mon Feb 25 2002 - 14:01:26 PST
