AMBER Archive (2005)

Subject: Re: AMBER: Fatal Error on loading a pdb in xLeap

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Jul 28 2005 - 22:56:32 CDT

Hi Kara,

Can you send the .pdb file? I had a simular problem when I tried to
download a .prepi file which was created using 'antechamber'. But the
reason was because of the bonds (I think). In a .pdb file, you dont have
those informations. It is just the atom names, and their coordinates
(with the residue name, etc.) which is loaded into xleap. I am curious why
that error message pops up even if you just load the .pdb file.

Best,

On Thu, 28 Jul 2005, Kara Di Giorgio wrote:

> I'm trying to load a pdb file with a carborane into xleap and it gives
> me the following error:
>
> !FATAL ERROR----------------------------------------
> !FATAL: In file [atom.c], line 444
> !FATAL: Message: bondAtomProblem found
> !
> !ABORTING.
>
>
> I've tried saving it out of the program that created the molecule
> (Spartan) as a mol2, but it gives me a message that 12 atoms are
> unknown to the format and do i want to replace them with dummy atoms (I
> can assume these are the boron atoms).
>
> (All in all, I've never been able to load a mol2 file into xleap that
> was generated by Spartan. I'm not sure why. I suspect it may be
> Spartan's fault as VMD also won't visualize those mol2 files.)
>
> Does anyone have any idea a) what the error on loading the pdb was and
> b) how to work around it to get my carborane created for use with
> amber?
>
> Thanks,
>
> Kara Di Giorgio
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
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