ADL: Amino acid protonation and explicit water

Marcus Fischer mf536 at york.ac.uk
Thu May 8 05:22:22 PDT 2008


Dear dockers/ Ruth/ Garrett,

to general questions:
(1) Is anybody aware of what the assumed pH for the standard settings is 
(I would assume 7)? In case one wants to consider the protonation state 
of amino acids at a different pH - for which amino acids (apart from 
His) would that be sensible and does manual correction result in a wrong 
calculation of respective charges (e.g. due to the lack of H-merging)?
and
(2) is random water placement considered in the docking simulation or am 
I right thinking that a sensible water analysis is advisable and 
cofactors should be included in the grid map calculation?

I would highly appreciate any hints,
Marcus


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