AMBER Archive (2005)

Subject: AMBER: Calculating of radius of gyration in Carnal

From: Hwankyu Lee (leehk_at_umich.edu)
Date: Sat May 14 2005 - 13:36:37 CDT


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.
---------
FILES_IN
 PARM p1 g5ace90.prmtop;
 STREAM s1 g5ace90-md01.mdcrd;
FILES_OUT
 TABLE t1 radgyr.tab;
DECLARE
 GROUP grpid1 (RES 1,2,3,4,5,6,7,8,9);
OUTPUT
 TABLE t1 grpid1%radgyr;
END
---------
I got an error like below.
---------

                          - CARNAL -
                          AMBER 8.0

                      COORDINATE ANALYSIS

input stdin
> FILES_IN
> 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.

best,
Hwankyu.

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