Re: AMBER: Leap problem

From: Kara Di Giorgio <>
Date: Thu, 14 Jul 2005 18:19:00 -0700

How would I make the prepin file for the Ni?

Would creating the Ni make loading the pdb not fail?

Kara Di Giorgio

On Jul 14, 2005, at 5:31 PM, Furse, Kristina Elisabet wrote:

> 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.
> G'luck,
> K
> 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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
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Received on Fri Jul 15 2005 - 02:53:00 PDT
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