AMBER Archive (2005)

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

From: David A. Case (case_at_scripps.edu)
Date: Thu Jul 28 2005 - 17:17:14 CDT

On Thu, Jul 28, 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.
>

There should be informative messages in the log, like "maximum coordination
exceeded...." that may be helpful. Do carbon atoms have a large number of
bonds in carboranes? Basically, the code in atom.c around line 385 triggers
a message when hydrogen has more than 1 bond, oxygen has more than 3 bonds,
or other elements have than 5 bonds. Does you molecule violate any of these?

As a test, you can try change line 385 in atom.c from "return(TRUE);"
to "return(FALSE);". I'm unsure whether or not defeating this test will
cause other problems or not....

...dac
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