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

From: Ilyas Yildirim <>
Date: Thu, 28 Jul 2005 23:56:32 -0400 (EDT)

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.


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
> !
> 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       -				-
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Received on Fri Jul 29 2005 - 05:53:00 PDT
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