Dear Yew Mun,
I would like to invite you to use R.E.D. Server Dev./R.E.D. Python at
http://q4md-forcefieldtools.org/REDS-Development/ (instead of R.E.D.
Server/Ante_R.E.D. 2.0 & R.E.D. IV).
In your case, I want to underline that R.E.D. Python will perform
entire FF generation for bioinorganic complexes:
Moreover, if you select MOD_GAUSSIAN_JOB = "Complex" the wavefunction
of the optimized geometry will be further tested and you will be able
to compute the frequencies if you set Freq_Calc = "On".
see
http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/Configuration.py
You might need to use geometrical constraints during the geometry
optimization step to conserve the geometry of the active site found in
the protein; just post a query in this case...
We also develop a specific charge model for bioinorganic complexes;
see RESP-X11 vs RESP-X1 and ESP-X1 associated or not with
modifications of MEPTHOD_OPTCALC, BASSET_OPTCALC, METHOD_MEPCALC &
BASSET_MEPCALC.
see once again
http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/Configuration.py
Finally R.E.D. Server Dev. uses a new version of the resp program (see
http://q4md-forcefieldtools.org/RED/resp/). You might find some
interests in the new RESP outputs.
regards, Francois
>> I'm not sure if this is the right place to ask about the R.E.D
>> server, so I'm just going to give it a shot.
>
> You can post your questions to the Amber mailing list or to the
> q4md-fft mailing list at
> http://lists.q4md-forcefieldtools.org/wws/info/q4md-fft as you wish.
>
>> I'm planning to simulate a zinc finger where the zinc ion is
>> coordinated to 4 other Cys residues. I plan to calculate the charge
>> of the Zn ion since coordination would definitely have changed its
>> +2 charge.
>
> If you want to have a +2 charge on the Zn(II) (not that obvious) you
> will have to set an intra-molecular charge constraint of +2 on this
> Zinc atom otherwise the atomic charges of Zn(II) is likely to be far
> lower than +2.
>
> See http://q4md-forcefieldtools.org/REDDB/projects/F-88/ to compare
> charges for Fe(III) with an integer charge value (i.e. +3) vs a
> non-integer charge value.
>
>> I know I can rely on the RED server for this, but under the charge
>> method (e.g. Resp-A1A), how do I know which one is suitable.?
>
> See http://q4md-forcefieldtools.org/REDS/popup/popkeyword.php
> RESP-A1A means HF/6-31G*//HF/6-31G*
> do you think HF/6-31G* is suitable for bioinorganic complexes?
> See once again: http://q4md-forcefieldtools.org/REDDB/projects/F-88/
> & http://onlinelibrary.wiley.com/doi/10.1002/cplu.201200141/abstract
>
>> Also, while the RED website has a tutorial for metal inorganic
>> complexes, is there a step by step guide as well on using the RED
>> server for deriving charges of metals in proteins.?
>
> See projects in R.E.DD.B.
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Received on Fri Jan 10 2014 - 00:00:02 PST
