AMBER Archive (2006)

Subject: Re: AMBER: Leap

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Jan 04 2006 - 16:02:20 CST

> Is there a way to turn off the option in leap that
> automatically adds missing heavy and hydrogen atoms?

It isn't an option.. you could change your residue name(s)
so that there would be no template to indicate missing atoms
to add, but then you'd be unable to saveamberparm.

The simplest way to enable saveamberparm would be to change
residue names in pdb and make templates for residues missing
undesired atoms. You would need to get new charges in this case,
or suffer from a broken charge model. Also the types of atoms
adjacent to the missing atoms would need to be updated.

Bill
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