Kara,
I did what Kristina described without any problems with a zinc ion bound
to a protein.
Here is my prepin entry for a zinc ion:
Zinc Ion
ZN2
ZN2 INT 1
CORR OMIT DU BEG
1.113744
1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000
2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000
3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000
4 ZN2 Zn M 3 2 1 1.0000 90.0000 180.0000 1.113744
DONE
This is an excerpt from a pdb file read into leap together with this
prepin file:
....
ATOM 8504 3HH3 NME 533 25.124 66.243 43.884
TER
ATOM 8505 ZN2 ZN2 534 52.861 45.180 39.638
TER
ATOM 8506 C14 FPP 535 40.449 46.478 41.663
....
A different issue is the question what charges to use for the nickel
which is bound to your organic molecules, and for those parts of the
molecule binding to the nicke atom...
Did you use the RESP procedure?
Oliver
Kara Di Giorgio wrote:
> 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 <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
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
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>>
>
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--
________________________________________________________________
Oliver Hucke, Dr.
Biomolecular Structure Center Health Sciences Building - K418C
Dept. of Biochemistry 1959 NE Pacific St.
University of Washington phone: (206) 685 7046
Box 357742 fax : (206) 685 7002
Seattle, WA 98195-7742 email: ohucke.u.washington.edu
________________________________________________________________
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Received on Fri Jul 15 2005 - 02:53:00 PDT
