AMBER: Leap problem

From: Kara Di Giorgio <>
Date: Thu, 14 Jul 2005 17:06:50 -0700

I'm trying to load an organometallic compound into Leap to create a
unit so I can then use that unit in DNA-binding simulations.

Here's my problem(s):

1. Antechamber doesn't know how to deal with nickel and therefore
won't create a prepin file. I CAN create a prepin file for the organic
portion of the molecule. I was planning on using this prepin file
along with a pdb file of the nickel and the 4 nitrogen atoms it's bound
to in the correct positions. I'd load the organic portion and then
load the pdb with the nitrogens named the same and have leap recognize
that they're from the organic portion and fill in the rest of the
molecule with the organic portion. I would then make the Ni-N bonds
and supply frcmod files, and manually correct the charges (in the
spreadsheet in Leap).

It ALMOST worked. When the organic portion is viewed in leap it's
correct. As soon as I load the pdb with the nickel and the nitrogens,
it does place most of the organic portion where it should be. Two of
the carbons in the crown-ether-like ring linking the nitrogens are WAY
out of position and this is tweaking the entire molecule. I tried
adding those two carbons to the pdb file (from the pdb file used to
generate the prepin file), but that made it worse.

I then thought I'd load the entire pdb file (organic and nickel
together) and go in and change all the atom types along with adding
charges, frcmod files and adding the Ni-N bonds. When I tried to load
the pdb file I got the following error message and Leap quit:

!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 444
!FATAL: Message: bondAtomProblem found

Does anyone have any other ideas as to what to do? I'm really stuck.


Kara Di Giorgio

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Received on Fri Jul 15 2005 - 01:53:00 PDT
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