AMBER Archive (2005)

Subject: Re: AMBER: problems with "protonate"

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Apr 11 2005 - 17:33:17 CDT

> It sounds easier to just let LEaP
> add the protons--but what command in LEaP does this?

Loadpdb does it automatically for residues that have templates
loaded in leap, such as the standard amber ff ones.

> Also, will LEaP be confused by the fact
> that it is an abnormal residue?

You need to create the template and load it. To get the initial
coordinates you could make a guess and let a qm or semiempirical
program minimize to a reasonable spot. Or use xleap to load a
pdb of the residue w/out H, set the bond types graphically, draw
in the H at a promising location, and use the leap cmd to fix
coordinates (I forget what the cmd is) using hybridization to set
the position.

Bill
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