AMBER: Calculating of radius of gyration in Carnal

From: Hwankyu Lee <>
Date: Sat, 14 May 2005 14:36:37 -0400

Dear Amber-users,

I'm trying to measure radius of gyration in Carnal (because it seems to be
unavailable in ptraj. Is it correct?). I followed the manual, searching this
forum, but got an error. My analin script is very simple like below.
 PARM p1 g5ace90.prmtop;
 STREAM s1 g5ace90-md01.mdcrd;
 TABLE t1;
 GROUP grpid1 (RES 1,2,3,4,5,6,7,8,9);
 TABLE t1 grpid1%radgyr;
I got an error like below.

                          - CARNAL -
                          AMBER 8.0

                      COORDINATE ANALYSIS

input stdin
> PARM p1 g5ace90.prmtop;
Reading parm file (g5ace90.prmtop)
parm: opening g5ace90.prmtop
> STREAM s1 g5ace90-md01.mdcrd;
Using default parm (g5ace90.prmtop) for STREAM s1
 (box will be read from stream)
 STREAM s1 g5ace90-md01.mdcrd;
Error in stdin line 3: STREAM: expected file name, got keyword: -
    Last token was -

It looks like something wrong with the input file. Could you tell me how to
handle this problem?
Thanks for your help in advance.


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Received on Sat May 14 2005 - 19:53:00 PDT
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