Dear Andrew,
Concerning new FF parameters you can find many information in
literature concerning the procedure itself but also already existing
parameters.
See ZAFF (
http://www.ncbi.nlm.nih.gov/pubmed/20856692); the program
developed by Guvench & MacKerell published in J. Mol. Model. 2008. You
might look at the approach based on 2nd derivative obtained by QM etc...
In general the bond & angle FF constants can be obtained from analogs;
using a new equilibrium value. For metal complexes dihedral are often
set to zero; see for instance the example in the AMBER contrib; the
heme example from D.A. Giammona, Ph.D. thesis ---dac 12/90. Defining
atom types around the metal complex can be tricky when once first
starts. Thus, two atoms which are equivalent but have different
equilibrium values should have a different atom types. Once again see
the Amber contrib...
regards, Francois
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 27 2011 - 01:00:03 PDT
