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

alexander yakovenko yakovenko_a at ukr.net
Thu Oct 17 12:11:39 CEST 2002

Hi Daan,

There is a problem. I have several examples like this with different initial position of H atom of OH ligands group, but even steepest descent algorithm doesn t find the interesting me energy minima for most of them. I have successfully found this minimum by AM1 SE, in all cases. I have see the parameters of LJ for N atom (ffgmx3nb.itp) and found them very similar to OA atom. I haven t calculated optimal r and E of pair N-H but it seems that such parameters was contribute to make N atom as a strong acceptor for H binding. 
If this is correct, would you please explain me how this parameters of N atom was chosen? 
How can I correct the ffgmx force field in this case?
Thank you,

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

> Clearly this is not the global energy minimum but a local one - the H
> connot flip the other way without moving through a lot of steric
> hindrance.
> cheers
> Daan

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