Ahmet
> Thanks for your reply/suggestion. But I wont use R.E.D. I will use
> Gaussian and Amber.
ok... R.E.D. Server Dev./R.E.D. Python interfaces Gaussian and
generate Amber force fields...
regards, Francois
> 26 Nis 2014 tarihinde 14:31 saatinde, FyD
> <fyd.q4md-forcefieldtools.org> ?unlar? yazd?:
>
>> 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 - 07:00:02 PDT
