AMBER Archive (2009)

Subject: Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old)

From: Ashish Runthala (
Date: Mon Jul 27 2009 - 04:09:23 CDT

Hello Albert,
The protons are removed to stabilize the protein confirmation,
removing the erroneous residues.

Always remember that, after any amino acid start from nitrogen (N) and
end on CG or CD groups, its correct indicating the proper link of
peptide bond with the next residue, but the erroneous protons are
removed after this CG or CD atoms.

For your simplicity, remember that the following atoms are generally
present as the erroneous protons after the CG or CD atoms, before the
N atom of the next residue starts in PDB file.So remove these entries
from pdb file.
Look at these atoms. All these are erroneous. Generally, such protons
are marked as
H, 1H,2H,3H, HA,HB,HC, HG1,HG2,HD1,HD2, 1HB, & 2HB.

 Remove such entries and protonate using leap for standard protonation.

Good Luck Albert,

On Mon, Jul 27, 2009 at 12:27 PM, albert albert
<> wrote:
> Dear Ross and all users,
> I would like to know, how can I proceed to remove proton in protein(Advanced
> Tutorials A1 old).
> Thanks for your response.
> regards
> Albert
> _______________________________________________
> AMBER mailing list

Ashish Runthala,
Faculty Division III,
Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031

_______________________________________________ AMBER mailing list