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