AMBER: Fatal Error on loading a pdb in xLeap

From: Kara Di Giorgio <>
Date: Thu, 28 Jul 2005 08:10:45 -0700

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


Kara Di Giorgio

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Received on Thu Jul 28 2005 - 16:53:01 PDT
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