AMBER Archive (2007)

Subject: AMBER: radius of gyration

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Fri Jan 26 2007 - 14:17:37 CST

Dear ALL,
 
 I am trying to calculate the radius of gyration by Carnal (AMBER8).
 I want to measure it through my md trajactory mdcrd file.
 Here is my simple input Analin file:
 FILES_IN
     PARM p1 prmtop;
     STREAM s1 mdcrd;
 FILES_OUT
     TABLE tab1 radgyr.tbl;
 DECLARE
     GROUP groupid1 (RES 1-5);
 OUTPUT
     TABLE tab1 groupid1%radgyr;
 END
 
But it shows errors in the output file, do you think it is because of my big mdcrd file? Thank you very much for your any advice!
 
  CARNAL -
                           AMBER 8.0
 
                       COORDINATE ANALYSIS
 
 
 input Analin
> FILES_IN
> PARM p1 prmtop;
 Reading parm file (prmtop)
 parm: opening prmtop
> STREAM s1 mdcrd;
 Using default parm (prmtop) for STREAM s1
  (box will be read from stream)
 stream: opening mdcrd.
> FILES_OUT
> TABLE tab1 radgyr.tbl;
> DECLARE
> GROUP groupid1 (RES 1-5);
 ** Group groupid1: 1340 atoms
> OUTPUT
> TABLE tab1 groupid1%radgyr;
> END
 (EOF reached on mdcrd)
 STREAM s1: no more files/crds (iteration 2500)
 SUMMARY
 (EOF reached on mdcrd)
 Internal error: stream file name 2 out of range
 

Esther B.

 
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