AMBER Archive (2007)

Subject: Re: AMBER: tleap crashing

From: David A. Case (case_at_scripps.edu)
Date: Tue Dec 11 2007 - 17:04:25 CST

On Wed, Dec 12, 2007, Ranjib Dey wrote:

> I trying to simulate a carbohydrate-protein complex using glycam06/ff94
> but , while saving *.prmtop and *.inpcrd files, tleap shows FATAL error and
> crashes, although "loadpdb" and "check" is not throwing any error.
> I am attaching the error message as well as the pdb file.

Unfortunately, we need more than just the pdb file to reproduce the error,
and hence to try to help. Can you provide a minimum set of commands, and all
the files you have loaded? Note that no one on the list is likely to have
access to glycam06.

[You can also anticipate getting e-mails saying "don't use ff94 anymore!", but
that is more a scientific issue than a likely cause of the crash.]

You could try to simplify the pdb file to narrow down the problem. Or, look
look at atoms 99 and 1914 (use savepdb to get a pdb file with the Amber
numbering and all of the hydrogens):

> !FATAL: Message: 1-4: cannot add bond 99 1914

Are those atoms supposed to be bonded together?

...dac
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