AMBER Archive (2009)

Subject: Re: [AMBER] connecting residues

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Jun 16 2009 - 11:37:33 CDT

> I would like to have your suggestion on how can I prevent the connectivity
> made automatically due to close contact .

Leap will not form bonds based on close contacts.

Other programs may infer bonds due to proximity and display them,
but these bonds don't exist in Amber.

Try viewing in xleap to see what bonds amber is creating. Ir may
be that somehow a bond exists for some other reason where there
is also a close contact.

Bill

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