Re: AMBER: Leap problem

From: Furse, Kristina Elisabet <>
Date: Thu, 14 Jul 2005 19:31:40 -0500

How about loading your prepin file for the organic portion, then a prepin for
the nickel as its own residue named NIC or something. Then load a pdb file with
the organic + Ni. In that pdb, have all of the atom names and residue name for
the organic part the same as in your prep file, then put a TER card, then the Ni
as a separate molecule, with its own residue name matching its prepin file. Then
leap will know what everything is, and you can use it to connect the two.

Quoting Kara Di Giorgio <>:

> 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.
> Thanks,
> Kara Di Giorgio
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Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse.Vanderbilt.Edu
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Received on Fri Jul 15 2005 - 01:53:01 PDT
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