AMBER Archive (2005)

Subject: Re: AMBER: Leap problem

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Fri Jul 15 2005 - 08:59:47 CDT

Thanks very much for all the help. I have gotten it to work now. I
also had to go into my pdb file and give all the atoms unique labels
matching the prepin file. I also had to add a ter between the nickel
and the rest of the organic portion otherwise xleap can't read it and
crashes. (I noticed that you had a ter in your pdb.)

Thanks again,

Kara Di Giorgio

On Jul 14, 2005, at 6:48 PM, Oliver Hucke wrote:

> 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_at_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_at_Vanderbilt.Edu
>>> ---------------------------------------------------------------------
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>>> The AMBER Mail Reflector
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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_at_u.washington.edu
> ________________________________________________________________
>
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