From: case <>
Date: Fri, 5 Mar 2010 07:50:47 -0500

On Fri, Mar 05, 2010, Asfa Ali wrote:
> *Leap added all 52 missing atoms according to residue templates,
> 52 H/ lone pairs
> The file contained 52 atoms not in residue templates
> Since added/missing = extra, there is a high probabilty of atoms
> with 'incorrect' names; you want to
> use addPdbAtomMap to map these names or change in files

This means the names of atoms in your pdb file are not the same as the names
of the atoms in Amber libraries. You need to fix this, usually by editing
the pdb file.

Be sure you are using AmberTools 1.3 (or have applied bugfix.12 to AmberTools
1.2.) These newer versions update Amber to the new pdb naming convention,
which *might* be the cause of your problem. But you definitely just have to
manually compare atom names in the pdb file to those in the library.

...good luck...dac

AMBER mailing list
Received on Fri Mar 05 2010 - 05:00:02 PST
Custom Search