Thanks for your reply/suggestion. But I wont use R.E.D. I will use Gaussian and Amber.
Ahmet Yıldırım
26 Nis 2014 tarihinde 14:31 saatinde, FyD <fyd.q4md-forcefieldtools.org> şunları yazdı:
> 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 - 05:30:03 PDT
