DEar Francois, unfortunately that time we have postponed that task, which was a mistake most probably because it turned out to be a biotarget of the compound of interest.
Can you please provide link on description of fitting to QM profile procedure? Is it possible to do such paraetrization for zinc binding using QM/MM methods in Amber?
Best regards,
Andrew
24.11.2009, 14:16, "FyD" <fyd.q4md-forcefieldtools.org>:
> 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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Received on Wed Oct 26 2011 - 05:30:03 PDT
