AMBER Archive (2009)

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

From: Andrew Voronkov (
Date: Tue Nov 24 2009 - 08:57:30 CST

Ok, then from protein crystallographic structures too. Can you please give any link on this QM profile fitting description. You mean that I can make for example QM/MM calculations for this part of the protein and then derive the required parameters from it?

Best regards,

24.11.09, 15:16, "FyD" <>:

> 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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