AMBER Archive (2009)

Subject: [AMBER] loading a following attached protein in amber 10

From: albert albert (albertassonke_at_googlemail.com)
Date: Tue Sep 08 2009 - 12:09:09 CDT

Dear users

greeting .

I don't know if you can help me to know why amber 10 cannot loading the
following attached file.

warm regards.

Albert

On Mon, Jul 27, 2009 at 11:09 AM, Ashish Runthala <ashish.runthala_at_gmail.com
> wrote:

> 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,
> Ashish
>
>
>
>
> On Mon, Jul 27, 2009 at 12:27 PM, albert albert
> <albertassonke_at_googlemail.com> 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
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> Ashish Runthala,
> Faculty Division III,
> Lecturer, Biological Sciences,
> Birla Institute of Technology and Science,
> Pilani, Rajasthan- 333031
> INDIA
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



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