Dear David,
Is any on-line tutorial-like document on how to check the antechamber produced files by hand? And what is the fucntion for the ligand-only md for checking the antechamber produced files?
Brett
At 2016-04-30 20:16:06, "David A Case" <david.case.rutgers.edu> wrote:
>On Sat, Apr 30, 2016, Brett wrote:
>>
>> Is the files for ligand md produced by antechamber highly reliable? Or I
>> still need check the files by naked eye?
>
>Depends. We often use antechamber files in "virtual screening" mode, where
>we live with whatever results we get, which are usually good, but not always
>so.
>
>If you have a single ligand that you are particularly interested in, it is
>still wise to examine the files by hand, and to run some ligand-only
>simulations to ensure that you are getting behavior that you can live with.
>
>If you have even more time, you can run quantum chemical calculations, and use
>programs like mdgx or paramfit to generate force fields tailored to your
>particular situation.
>
>...dac
>
>
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Received on Sat Apr 30 2016 - 21:00:03 PDT
