AMBER Archive (2006)

Subject: AMBER: carnal prob

From: bala (cbala_at_igib.res.in)
Date: Thu May 04 2006 - 02:44:53 CDT

dear amber users,
 
i wanted to use hbond analysis in carnal. I am using Amber8. i hve pasted below my input and output file. Kindly suggest me what could be the problem. i hve checked the path of topology file and co-ord file. everything is correct.
 
input
-------------------------------------------------------
FILES_IN
  PARM p1 at-oct.prmtop;
  STREAM s1 traject/vp1.mdcrd.gz;
FILES_OUT
  HBOND h1 accpt LIST;
  HBOND h2 Donr LIST;
DECLARE
  GROUP g1 (RES 10);
  GROUP g2 (RES 25-5223);
OUTPUT
  HBOND h1 DONOR g2 ACCEPTOR g1 STATS;
  HBOND h2 DONOR g1 ACCEPTOR g2 STATS;
END
---------------------------------------------------------------
output
---------------------------------------------------------------
- CARNAL -
                          AMBER 8.0
                      COORDINATE ANALYSIS

input stdin
> # HBOND analysis
> FILES_IN
> PARM p1 at-oct.prmtop;
Reading parm file (at)
parm: opening at
at: does not exist (nor do .Z or .gz)
---------------------------------------------------------------
 
thanks in advance,
c.bala

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu