On Wed, Sep 22, 2010, Joe Bozell wrote:
> 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.
Ordinarily, you would just use antechamber for a *single* molecule; once you
have the prepi or mol2 file it creates, you load that into LEaP, and use
loadPdb to read in the pdb file. The multiple copies part has nothing to do
with antechamber.
(Nevertheless, even with bad input, antechamber should not segfault. If you
can post your inputs, we can try to figure out what is going on.)
....dac
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Received on Wed Sep 22 2010 - 13:30:04 PDT
