[phenixbb] Elbow ligand building
krahn at niehs.nih.gov
Wed Nov 4 09:35:01 PST 2009
I am having some problems building ligand parameters with elbow.
I have an accurate reference structure, but elbow seems to "regularize"
the coordinates in a way the distorts the structure. Is there a way to
With --opt, QM optimization should hopefully remove distortions, but it
is not doing a very good job for this molecule. So, I decided to
optimize using Gaussian, and a better basis set.
It seems that the Gaussian interface is still fairly simple, and it
seems that you have to edit the Gaussian.csh template. So, I did that,
but got the "Gaussian does not seem to be installed" message.
Unfortunately, elbow runs the Gaussian script with output to /dev/null,
so there is no way to see any error messages. Maybe that should be done
only when the --quiet flag is given.
I edited the Python source to let errors go to the tty, and found that
the problem is in the way the script is invoked using "csh -c %s.csh".
That only works if "." is in your $PATH, which is often the case. It
also invokes an extra instance of csh, because it is invoked as a system
command. The correct way to run a shell script is to leave out the '-c'.
Elbow makes the script executable, so an even better approach is to just
leave out "csh", and do "os.system('./%s.csh' % project)". Then, the
script can be in sh/bash/etc. Maybe the was the intent of using '-c'?
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