AMBER Archive (2009)

Subject: Re: [AMBER] non standart residue library creation with tleap (Zn atom)

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Nov 24 2009 - 08:16:54 CST

Andrew,

> Can you please say why I can't just measure bond lengths and
> dihedral angles parameters in the PDB structure which I want to use
> for MD. This will just fix the already existing parameters and that
> is what I need. Why I should gather or calculate prceise bond length
> and angle parameters if the PDB data already measured by X-ray
> analysis? The bond energies and VdW radii I can get from the papers,
> yes.

You can get equilibrium values for bonds & angles from small
crystallographic structures, Yes. Dihedrals do not have equilibrium
values. Force constants for bonds and angles and dihedral parameters
can be obtained from fitting to a QM profile.

regards, Francois

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