possible bug in carnal in AMBER5

From: Michael G Cooney <chemgc_at_panther.Gsu.EDU>
Date: Wed 17 Oct 2001 17:00:01 -0400 (EDT)

Dear Amber users,

I've recently used both AMBER 5 and 6 (on different machines) and have
noticed that the carnal module in AMBER 5 doesn't remove the waters from
MD coordinate files while the one in version 6 does. The input files I use
are something like:

# strip waters from mdcrd file
  PARM p1 start_wat_23Na10Cl.prmtop;
  STREAM s1 mdeq300ramp50.mdcrd restart100_300.mdcrd;
  COORD c1 first200ps_nw.mdcrd CRD;
  GROUP grp1 (RES 1-53);
  COORD c1 s1;

I should probably put a reference to the group declaration in my OUTPUT
direction line (COORD c1 s1 ???) but carnal rejects any input beyond the
s1 token. It runs but just gives me back a merged crd file with all
residues including waters still in it. As I remember a similar file did
work in Amber 6, though.

Thanks very much for any help...probably I'm missing the correct
declaration of residues.


Michael G. Cooney, Ph.D.
Dept. of Chemistry
Georgia State University
Atlanta, GA 30303
Received on Wed Oct 17 2001 - 14:00:01 PDT
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