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