AMBER: Carnal & Radius of gyration

From: <>
Date: Tue, 12 Oct 2004 16:29:26 -0500
('binary' encoding is not supported, stored as-is) Dear Amber Community,

I am trying to obtain the radius of gyration of a molecule I have
simulated. According to the below website, it is possible to do this with
carnal. I am using Amber7.
I have set up the following "script":
 PARM p1 tmp56.prmtop
 STREAM s1 tmp56_bio_md3.restrt.4
 TABLE p1 s1%radgyr

and get the following output/error message:
                          - CARNAL -
                          AMBER 6.0

                      COORDINATE ANALYSIS

> PARM p1 tmp56.prmtop
Reading parm file (tmp56.prmtop)
parm: opening tmp56.prmtop
> STREAM s1 tmp56_bio_md3.restrt.4
 STREAM s1 tmp56_bio_md3.restrt.4
Error in line 3: PARM: expected ';'
    Last token was STREAM

Why does it say Amber 6.0? I have Amber7 installed and had received the
CD last November/December, shouldn't that have included Carnal 7.0?
More importantly, what do I have to do to the script I have to get a
radius of gyration for my molecule? The input is a prmtop file, and the
restart file at the end of the simulation.
Thanks for your help.

Best Regards,


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Received on Tue Oct 12 2004 - 22:53:00 PDT
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