[phenixbb] Elbow ligand building

Joe Krahn 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 
disable this?

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'?

Joe Krahn

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