AMBER Archive (2006)

Subject: Re: AMBER: Leap adds hydrogens but cannot resolve their type.

From: David A. Case (
Date: Thu Aug 10 2006 - 15:15:16 CDT

On Thu, Aug 10, 2006, Paul R Brenner wrote:
> Created a new atom named: H within residue: .R<NLYS 1>
> Created a new atom named: HB1 within residue: .R<NLYS 1>

These messages mean that your pdb file has atoms named "H" and "HB1" that are
not a part of the standard resiudes in Amber. You need to make sure that
the atom names in the pdb file match those in the Amber residue libraries.

The simplest way to do this is just to strip hydrogens from input pdb file
and allow LEaP to build them back in. An alternative is to use protonate
with the "-k" flag; this will preserve the positions of the hydrogens you
have, but update their names to the Amber (and IUPAC) standard.


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