AMBER: Question about Boron

From: Kara Di Giorgio <>
Date: Wed, 14 Mar 2007 10:15:22 -0700

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

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
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