AMBER Archive (2007)

Subject: Re: AMBER: Problem with LEaP generating topology and coord files after double bond creation

From: David A. Case (case_at_scripps.edu)
Date: Wed Nov 21 2007 - 19:08:08 CST

On Wed, Nov 21, 2007, M. L. Dodson wrote:
>
> I am including the LEaP script and the key part of the log file.
> I think it hangs generating the topology because the bond created
> is a double bond.

The only use Amber would make of whether this is a double bond or not is
in visualizing it in edit mode. That information gets lost by the time the
prmtop file is made.

So, you should certainly see if not specifying this as a double bond would
change anything.

Eventually, we need to get the files you used, so that we can try to reproduce
the problem here.

> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> <program hangs here, using 100% CPU>

This sounds evil -- somehow the tree-walking routine has probably got lost.
Frustrating, because again this information is not really used for anything.

I'd be very curious to know calling the cross link a double-bond is causing
the problem...we might be able to track that one down.

...thanks for the report...dac

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