[AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ?

From: Marek Maly <marek.maly.ujep.cz>
Date: Tue, 20 Apr 2010 21:54:04 +0200

Dear all,

just a quick technical question. I am just wondering
what is the recommended way of preparing protein structure
for simulation in explicit water under given pH.

If I am not wrong, in this case simulation under constant pH
has to be approximated by simulation with fixed "correspondent"
protonation state of the given protein. Am I right ?

If yes, what is the recommended procedure for protein protonation
respect to given pH ?

It is for example sufficient to use just H++ server to assign protonation
to all ionisable groups regarding to given pH and of course regarding to
the given
(representative) protein conformation ?

Speaking about H++ it is OK to keep their default value of internal
protein dielectric constant which has the
value 6 or one have to change it to value 1 which is the only recommended
value in any Amber implicit solvent
calculation including MM/PBSA which I would like to carry out with my
protein/X complex after explicit water MD ?

Thanks a lot in advance for any valuable comments/experiences !

Best wishes,


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Received on Tue Apr 20 2010 - 13:30:03 PDT
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