Re: [AMBER] on antechamber

From: Brett <>
Date: Sun, 1 May 2016 11:51:58 +0800 (CST)

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?


At 2016-04-30 20:16:06, "David A Case" <> 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
>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.
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Received on Sat Apr 30 2016 - 21:00:03 PDT
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