AMBER Archive (2009)

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

From: Bo Baker (ratuma2009_at_gmail.com)
Date: Wed Jan 07 2009 - 20:18:02 CST

Hi,

> This usually means that the atom names in the pdb file don't match the
atom names in the library for that residue.

I notice this. But I don't know which amber library to look at? And if the
atom name in the pdb file can't be found in the library, how could the atom
be converted to the amber type? it may need some deep knowloadge on
chemistry and the forcefield.

Thank you

Bo

On Thu, Jan 8, 2009 at 12:08 AM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> 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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