Re: [AMBER] Calculation of charges, force constanst, bonds, angles of a ligand using antechamber and gaussian

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Sat, 26 Apr 2014 13:31:12 +0200

Dear Ahmet,

See
http://q4md-forcefieldtools.org/REDServer-Development &
http://q4md-forcefieldtools.org/REDServer-Development/Documentation &
http://q4md-forcefieldtools.org/REDServer-Development/Documentation/Configuration.py
&

- Create a Configutation.py & write in it:
CHR_TYP = "RESP-X1"
# To use the density of MEP points defined by U. Ryde
SURFMK_MEPCALC = "IOp(6/33=2,6/41=10,6/42=17)"
FFPARM = "AMBERFF99SB"
# then you might test (be patient here):
MOD_GAUSSIAN_JOB = "Complex"

- You might need to create a Project.config file if the total charge
and spin multiplicity of your molecule does not equal 0 and 1,
respectively:

MOLECULE1-TOTCHARGE = your-case
MOLECULE1-SPINMULT = your-case

- create an archive file:
zip archive.zip Mol_red1.pdb Configurration.py
  or
zip archive.zip Mol_red1.pdb Configurration.py Project.config

- upload at:
http://q4md-forcefieldtools.org/REDServer-Development/upload-log.php

- in case of a problem request for a private assistance at:
http://q4md-forcefieldtools.org/REDServer-Development/help-log.php
  or a public help in the Amber or q4md-fft mailing list
http://lists.q4md-forcefieldtools.org/wws/info/q4md-fft

regards, Francois



> 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.


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Received on Sat Apr 26 2014 - 05:00:03 PDT
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