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 <kdigiorgio.sbcglobal.net>:
> 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
> !
> !ABORTING.
>
>
> 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
