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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Wed Feb 12 2014 - 06:00:04 PST
