AMBER Archive (2008)

Subject: Re: AMBER: autodock pdb to obtain parm with tleap

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 27 2008 - 12:25:02 CST

On Wed, Feb 27, 2008, Henar Martínez wrote:

> The pdb file is:
> >ATOM 12 1H15 MOL 371 -13.656 -0.706 4.895 1.00

Here is an atom named "H151"

> The prep file:

....does not contain any atoms named H151...

> >Loading PDB file: ./mdb.pdb
> >-- residue 371: duplicate [ H12] atoms (total 2)
> >
> > ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
> > (same-name atoms are reduced to a single atom)
> >
> >Created a new atom named: H151 within residue: .R<MOL 371>

LEaP is warning you that all atom names within a given residue must be
unique. It also notes that the pdb file has an H151 atom that is not found
in the prep file, so it tries to create it.

> >WARNING: There is a bond of 3.872151 angstroms between:
> >------- .R<MOL 371>.A<C21 66> and .R<MOL 371>.A<C23 75>

There are lots of warnings like this. Maybe it is all related to the naming
problem.

> >FATAL: Atom .R<MOL 371>.A<H151 81> does not have a type.

LEaP doesn't know what to do with atom H151.

Bottom line is that the atom names in the pdb file must exactly match the
atom names in the prep file. Once you do this, you have a chance to go
further.

...dac

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