AMBER Archive (2006)

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

From: Paul R Brenner (pbrenne1_at_nd.edu)
Date: Tue Aug 15 2006 - 10:39:08 CDT

Thank you. Your recommendation to delete all initial hydrogens from the pdb
worked. The fact that the pdb loaded without comment on the missing 'names'
let me to erroneously believe that the newly xleap added hydrogens were
'nameless'

Thanks again,

Paul

Quoting "David A. Case" <case_at_scripps.edu>:

> 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.
>
> ...dac
>
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