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

alexander yakovenko yakovenko_a at ukr.net
Mon Oct 14 15:48:22 CEST 2002

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.

Thank you,

Alexander Yakovenko
Institute of Molecular Biology & Genetic of NAS of Ukraine
acad.Zabolotnogo str. 150
E-mail: yakovenko_a at ukr.net  

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