I am attempting to use Amber for MD runs on a collection of small molecules
to observe their interaction during a self assembly process. I am able to
carry out MD runs on a single molecule in a water shell using antechamber
and subsequent steps. However, how does one carry out the same process on
multiple copies of a single molecule within a solvent box?
I have a pdb file for a pair of these molecules, and have used antechamber
to generate a prepi file. However, parmchk on the resulting file gives a
"segmentation fault" message, suggesting that the number of atoms may be too
large.
Is there a general method for carrying out this type of experiment within
Amber?
Thanks,
Joe Bozell
University of Tennessee
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Received on Wed Sep 22 2010 - 11:30:04 PDT
