AMBER Archive (2006)

Subject: AMBER: Zinc-coordinating histidine protonation state

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Thu Jul 27 2006 - 15:01:16 CDT

Dear amber users,
   The zinc-coordinating Histidine in my NMR structure does not have
any hydrogen (neither on delta nor on epsilon nitrogen) where as the
other non-zinc-coordinating histidines have delta protonation (HID).
So, I was wondering what is usually the protonation state of the
histidines that coordinate zinc (HID or HIE)?

And also what is the default protonation state oh histidine in amber?
If I say HIS, does amber take it as HIE or HID?

thanks a lot in advance,
Rgds,
Nitin

On 27/07/06, Nitin Bhardwaj <nbhardwaj_at_gmail.com> wrote:
> Dear Ross,
> thanks a lot for that instant reply. I followed that text in that
> mail closely, and I could get xleap to recongnize my zinc atom.
>
> thanks,
> Nitin
>
> On 27/07/06, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> > Dear Nitin,
> >
> > > http://structbio.vanderbilt.edu/archives/amber-archive/2004/4188.php
> > > loadamberparm frcmod.zna
> > > it gives an error "syntax error"
> >
> > This was a typo in the original message it should be loadamberparams.
> >
> > > after this, when i load my protein with zinc, it still can not
> > > identify the zinc atom.
> >
> > The frcmod file only describes the non-bond parameters and mass of the zinc.
> > It does not include the charge or atomic element of the zinc. You need to
> > follow the text in the original message you reference more closely. You need
> > to create a unit in Leap called ZNA and make the atom type ZN. Save it as a
> > lib file with saveoff. Then you need to change the zinc residue name in your
> > protein to be ZNA. Load leap, load the frcmod file, load the lib file then
> > load your protein.
> >
> > Note, if you explicitly want to bond residues to the zinc then you will need
> > to also provide bond, angle and dihedral parameters in the frcmod file.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | HPC Consultant and Staff Scientist |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> > be read every day, and should not be used for urgent or sensitive issues.
> >
> >
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>
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> $B&-(BI+I$B'*(B
> 

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