Re: [AMBER] Parametrization of the protein with the assigned protonation states

From: Jason Swails <>
Date: Wed, 04 Jun 2014 10:35:02 -0400

On Wed, 2014-06-04 at 15:43 +0200, James Starlight wrote:
> Thanks Jason!
> As I've noticed pdb2pqr server have assigned exactly such names to the
> titrable residues. The only issue id sue to the some problems with some
> hydrogen types added by the server to my pdb
> FATAL: Atom .R<NSER 64>.A<H 14> does not have a type.
> FATAL: Atom .R<CYM 112>.A<HN 11> does not have a type.
> FATAL: Atom .R<CYM 218>.A<HN 11> does not have a type.
> Does it possible to ignore all hydrogens presented in the processed in
> such pdb allowing leap to add it to the structure again?

Yea, delete them from the PDB.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jun 04 2014 - 08:00:03 PDT
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