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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.
http://amber.ch.ic.ac.uk/archive/200310/0241.html
I have set up the following "script":
FILES_IN
PARM p1 tmp56.prmtop
STREAM s1 tmp56_bio_md3.restrt.4
OUTPUT
TABLE p1 s1%radgyr
END
and get the following output/error message:
- CARNAL -
AMBER 6.0
COORDINATE ANALYSIS
input carnal.in
> FILES_IN
> 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 carnal.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,
Armin
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Received on Tue Oct 12 2004 - 22:53:00 PDT
