Re: AMBER: Torsion terms in xleap

From: David A. Case <>
Date: Mon, 17 Sep 2007 19:35:24 -0700

On Mon, Sep 17, 2007, Lili Peng wrote:
> My apologies for the repeat question :). However, I did try to do the
> "pre-processing" of the mol2 file in antechamber before I sent the original
> email, but I ran into a problem with loading the prepi file in xleap.

As Junmei has explained, the problem lies in the fact that your starting
geometry is just bad enough that antechamber mis-assigns bonds. Junmei's
workaround does not appear to have worked for you, and I don't have any
practical suggestions other than: get a better starting structure.

> x = loadamberprep glu4_linear_PTX.prepi

This is not the correct syntax: type "help loadAmberPrep" at the LEaP prompt.

But that won't solve your structure problem....


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Received on Wed Sep 19 2007 - 06:07:29 PDT
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