AMBER: radius of gyration

From: Esther Brugger <>
Date: Fri, 26 Jan 2007 12:17:37 -0800 (PST)

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:
     PARM p1 prmtop;
     STREAM s1 mdcrd;
     TABLE tab1 radgyr.tbl;
     GROUP groupid1 (RES 1-5);
     TABLE tab1 groupid1%radgyr;
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!
                           AMBER 8.0
                       COORDINATE ANALYSIS
 input Analin
> 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.
> TABLE tab1 radgyr.tbl;
> GROUP groupid1 (RES 1-5);
 ** Group groupid1: 1340 atoms
> TABLE tab1 groupid1%radgyr;
 (EOF reached on mdcrd)
 STREAM s1: no more files/crds (iteration 2500)
 (EOF reached on mdcrd)
 Internal error: stream file name 2 out of range

Esther B.

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Received on Sun Jan 28 2007 - 06:07:47 PST
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