I'd like to know if anyone has any experience with Boron in Amber. I'm
trying to see if I can make and use a p-carborane structure.
So far I've made the p-carborane in another program and optimized it
using QM calculations. This gave me positions, angles, charges, etc.
I've re-made the carborane in xLeap using the pdb generated by my QM
calculations and made a frcmod file for it. I created the Amber input
files and ran a MD simulation with just the p-carborane and it held
together (good sign).
I want to put the p-carborane in place of a phenyl ring on a molecule
and run MD to see what happens. I have a pdb file with the molecule
and have edited it to remove some atoms of the phenyl ring and re-name
the parts that correspond to the carborane portion. I load the
individual portions into xLeap and then try to load the pdb file. At
this point, xLeap crashes. I'm not quite sure why. The program just
quits.
I'm using Amber 8 on a Macintosh G4.
Any help would be greatly appreciated.
Thank you,
Kara Di Giorgio
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Received on Sun Mar 18 2007 - 06:07:09 PDT
