Dear Users,
I am trying the following procedure but I have a problem.
http://www.teokem.lu.se/~ulf/Methods/resp.html
*Step 1:*Optimise the molecule with QM methods, typically B3LYP/6-31G*.
*My step 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(d)-Submit
*Step 2:*Calculate the electrostatic potential. For the Amber-99SB force
field, this should be done at the HF/6-31G* level (B3LYP/6-31G* if you have
metal sites). Other force fields require other levels of theory.
*My step 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(d)-Additional Key
Words:Pop=MK
IOp(6/50=1)-Submit.
I get "Severe error 2070 message" in Step 2. I am using Gaussian 09
Revision-C.01. Where is my mistake?
*My step 3:* Finally I will use antechamber in this step.
Thanks in advance
2014-04-25 11:26 GMT+03:00 Karl Kirschner <k.n.kirschner.gmail.com>:
> 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
>
--
Ahmet Yıldırım
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Received on Sat Apr 26 2014 - 00:30:03 PDT
