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Re^3: Tips to run Docking/ doping Calculations using Firefly-8.0.1

Siddheshwar Chopra
sidhusai@gmail.com


Dear Sanya,
Thank you for your guidance. I agree with you that I must check up for the forcefield needed for my system. My system consists of carbon atoms and I feel UFF will be sufficient.
But in general, Sanya I strongly feel regarding my DOCKING question; that I must ATLEST get systematic results whether I use UFF, Ghemical etc. consistently for various sites. What do you say about this? I mean the results must have some systematic error when same forcefield is used. I need to know whether this would be good enough to predict/shortlist the binding site? Also I agree with you that parameterizing the forcefield would me more tedious.
What do you say about the forcefields MMFF94 and MMFF94s?


Kind Regards,


On Sun Dec 21 '14 3:55am, sanya wrote
-------------------------------------
>The quality of MM calculations depends on the force field used. First of all, you should search the literature to find whether the force field you chose is good for your compounds. AFAIK, UFF is commonly used for inorganic substances. It may happen so that some important force field parameters are absent for your molecules, and you'll have to parameterize the force field manually (based on DFT calculations). It may be even more difficult that performing DFT calculations directly :)

>On Thu Dec 18 '14 8:00pm, Siddheshwar Chopra wrote
>--------------------------------------------------
>>Dear Alex,
>>Please answer this question Sir. I really need to know this. I need your guidance here. Is it sufficient to run MM for concluding the docking site on the base layer? Oncr it is confirmed, then I would prefer to run dft for sprcific properties.

>>Kind Regards,
>>
>>
>>On Thu Mar 6 '14 10:28am, Siddheshwar Chopra wrote
>>--------------------------------------------------
>>>Dear Sir,
>>>Ever since I have started working on Firefly, I have been thinking of studying the doping and docking phenomena on various samples. But because DFT is a really expensive calculation, so I am on the backfoot. Could you please suggest me a simpler way to find the doping or docking sites for any foreign atoms on any molecules?
>>>Point me if I am wrong.... Does this solve my purpose if I attach the foreign atom on various sites of molecule under study and run MM calculations? Of course it will not give me accurate energies but is it sufficient to conclude and comment on the favourable doping/docking site? And then can run more accurate DFT calcs for other properties?

>>>Regards,


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