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

[Daan Virtual]

Alexander

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.

Daan


On Sun, 13 Oct 2002, alexander yakovenko wrote:

> Hi all,
> Do you know anything about correct parameterization of N atom type if ffgmx force field?
> I work with protein - ligand complexes and found effective H-bonding of peptide N atom of protein. But N peptide atom  is not good for H-bonding in case presence pseudo double bond with CO group with previous residue in protein.
> Is this a gromacs error ?
> 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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