AMBER Archive (2005)

Subject: AMBER: Leap question

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Thu Jul 14 2005 - 10:10:12 CDT

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
calculations.

Thank you,

Kara Di Giorgio

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