Re: [AMBER] about protonation state check.

From: Brian Radak <radak004.umn.edu>
Date: Wed, 12 Feb 2014 08:37:48 -0500

Tleap will assign protonation states based on the residue name (which in
turn takes information from the appropriate "lib" file). This is only as
scientific as the user makes it. The other programs you mention are
probably a great place to start.

A good alternative, especially if you are using implicit solvent, is to use
constant pH MD. You can read about it in the AMBER manual.

Regards,
Brian


On Tue, Feb 11, 2014 at 7:15 AM, setyanto md <stwahyudi.md.gmail.com> wrote:

> Dear All, amber user adn developer.
>
> If I have protein without metal, and I like to simulate in various
> temperature, 300K, 400K and 500K, then should I check the protonation state
> of mya charged residue first ? by using PROPKA or H++ webservice ?
>
> is tleap also detect a false protonation state of charged residue ?
>
> Thank you.
>
> best regards,
>
> Setyanto tri wahyudi
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



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 Brian Radak                                             :     BioMaPS
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Received on Wed Feb 12 2014 - 06:00:04 PST
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