Hello Ahmet,
Regards to the force constants for internal coordinates (bonds, angles,
torsions) - I don't think you will be able to do this easily using your
workflow. A single optimized structure will not easily provide you with MM
force constants that are balanced with an existing force field. Typically
to obtained optimized parameters for internal coordinates one needs to do
several QM calculations that scan along the degree of freedom that you are
interested in. For example if you want to optimize a bond parameter, you
would do several QM constrained optimizations that constrain the bond at
different lengths; then you would iteratively fit the MM bond force
constant to reproduce the QM relative energies. If this doesn't sound
familiar, take a look at some parametrization papers to familiarize
yourself with it. You could also create a user account on
www.wolf2pack.comand take a look at the Knowledge Modules there that
explain these ideas in
a little more detail.
Regarding partial atomic charges - you may want to elaborate on if you
received an error when using antechamber, and what that error is. You may
also want to consider using R.E.D.
Best regards,
Karl
On Fri, Apr 25, 2014 at 10:07 AM, Ahmet yıldırım <ahmedo047.gmail.com>wrote:
> Dear users,
>
> I have a small ligand including 18 atoms. I want to calculate all
> parameters(charge,force constant,bond,angels) of this ligand for amber99
> force field.
> 1.) I optimized that ligand using Gaussian09
> (GaussView-Calculate-Gaussian Calculation Setup-Job
> Type->Optimization-Method-Ground State->DFT->Default Spin->B3LYP-Basis
> Set->6-31G-Submit
> 2.) For Calculation of electrostatic potential:
> Gaussview-Open-optimized .chk file
> Calculate-Gaussian Calculation Cetup-Job Type->Energy-Method-Ground
> State->Hartree-Fock->Default Spin->-Basis Set->6-31G-Additional Key
> Words:Pop=MK
> IOp(6/50=1)-Submit
> 3.) Now I will use antechamber. But There arent force constants,
> dihedral,bonds.. in Gaussian output file.
> ...
> # hf/6-31g geom=connectivity iop(6/50=1) pop=mk
> -----------------------------------------------
>
> Where is my mistake?
>
>
> --
> Ahmet Yıldırım
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Karl. N. Kirschner, Ph.D.
Research Consultant: Bonn-Rhein-Sieg University of Applied Sciences
Guest Researcher: Fraunhofer SCAI
Sankt Augustin, Germany
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 25 2014 - 01:30:04 PDT
