AMBER: Leap question

From: Kara Di Giorgio <>
Date: Thu, 14 Jul 2005 08:10:12 -0700

I'm trying to model an organometallic compound. when I tried to run my
compound through antechamber, it didn't know how to handle the nickel
so I ran the organic portion and got a prepin file. My original idea
was to load the organic portion, then the nickel from the original pdb
file and then create the bonds in xLeap. My problem is that I can't
get the nickel to come into xLeap in the correct position. I've tried
creating a pdb file with the nickel and its coordinating nitrogen
atoms, but xLeap keeps crashing when I try and load the pdb after I've
loaded the organic prepin file. Does anyone have any ideas for getting
the info into xLeap? I have frcmod files that I want to load after I
re-assemble the molecule and I'm not interested in the charges from the
prepin file as I'm going to edit them in xLeap based on previous

Thank you,

Kara Di Giorgio

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Received on Thu Jul 14 2005 - 16:53:00 PDT
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