[gmx-users] parameterization of N atom type if ffgmx (continue)

[Daan Virtual]

Hi Alex

It sounds to me like the OH of your ligand is DONATING a hydrogen bond
to the ND1 of the histidine and ACCEPTING a hydrogen bond from your
backbone nitrogen - there is nothing wrong with that?

cheers

Daan


On Mon, 14 Oct 2002, alexander yakovenko wrote:

> Hi again,
>
> >It all depends what you mean with "H-bonding" - the backbone nitrogen is
> >an excellent hydrogen bond donor (if it wasn't, such a thing as protein
> >secondary structure wouldn't exist), but cannot accept hydrogen bonds.
>
> There is problem. I have found that after minimization the H atom of OH group of ligand located at 2.48A, O atom at 2.45A from N of backbone and at 3.07 from H atom to ND1 atom of HIS residue. The angle of backbone N   H of OH group of ligand -ND1atom of HIS is 82 degrees. I thing that Gromacs detect backbone N - H of OH group as H-bond, than this system is really minimized. The AM1 optimization of this system give the correct position of H atom : backbone N - H 3.05A, ND1 - H 2.61A.
> So it seems that backbone N is parameterized as acceptor for H-bonding.
> >Daan
>
> Thank you,
>
> Alexander Yakovenko
> Institute of Molecular Biology & Genetic of NAS of Ukraine
> 03143
> acad.Zabolotnogo str. 150
> Kiev
> Ukraine
> ______________________________________________
> E-mail: yakovenko_a at ukr.net
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

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