AMBER Archive (2000)

Subject: carnal script

From: Peter Gannett (pgannett_at_hsc.wvu.edu)
Date: Wed May 10 2000 - 08:37:37 CDT

Dear Amber users:

We're back to trying to use carnal and we could use some help. We are trying to write out a normal vector to a plane described by three atoms (#s 256-258) in a trajectory into a CRD file (or PDB). Our carnal input file (analin) looks like what is below. All that gets written to the file cno2.pdb is CARNAL dump. So, it looks like we've screwed up something between the DECLARE and OUTPUT statements so that there is nothing to write. We've played around a bit with this but other that generating errors, no luck. Any suggestions. Thanks.

FILES_IN
  PARM p1 tat5m_md_nowatNA.top;
  STREAM s1 tat5m_md_nowatNA.traj;
FILES_OUT
  COORD crd cno2.pdb CRD;
DECLARE
  PLANE pn1 256 257 258;
OUTPUT
  COORD crd s1 SELECT (256-258);
END