Re: [AMBER] use of packmol in amber

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Mon, 13 Dec 2010 20:41:20 -0800

> My command line is
> $AMBERHOME/exe/sander -O -i -o min.out -p -c
> mixture_32.crd -r min.rst
> We tried it two-three times but no out put is created. Why????

In this situation one would expect to see a message printed by the
program or the operating system explaining what the problem is.
This is why I asked you to copy/paste the command line and the
result. So I expect to see something like this:

$ $AMBERHOME/exe/sander -O -i -o min.out -p -c mixture_32.crd -r min.rst
AMBERHOME: Undefined variable.

to give one possibility. Note the presence of the two '$' shell
prompts - these indicate that everything from the beginning to the
end of program invocation have been copied and pasted. Without
seeing that, it is impossible to know whether you are simply
overlooking the diagnostic message, or whether there is no such
message, which would be very unusual.


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Received on Mon Dec 13 2010 - 21:00:06 PST
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