AMBER Archive (2009)

Subject: Re: [AMBER] Re: AMBER: ligand parameter

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Jan 07 2009 - 07:08:27 CST

On Wed, Jan 07, 2009, Bo Baker wrote:

>
> I notice that when I load the protein, amber add some atoms. When I try to
> save amberparm, it complains the bond problems with these added atoms. At
> the end, the parm was created and saved.

This usually means that the atom names in the pdb file don't match the
atom names in the library for that residue. Unless LEaP is just adding
hydrogens (or things like OXT atoms) that you know are missing, you will
need to fix this.

....dac

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