Dear Ambers,
> earlier this week I asked some questions about the preparation of protein
> structures prior to MD simulations with respect to the treatment of
> titrable residues and the placement of counter ions.
> I would like to thank Michal Otyepka, Malcolm Gillies, Deepak Singh, Rick
> Venable, Mike Ford, and Kenward Vaughan for their kind responses.
>
> Christian
>
last year appeared paper entitled "Modification of the GB model Suitable
for Macromolecules, Onufriev A., Bashford D., Case D.A., J.Phys.Chem. B
2000, 104, 3712-3720" dealing with computation of pK shifts for titratable
residues in lysozyme, myoglobin, and bacteriorhodopsin. The improved GB
method was incorporated to MEAD package (
http://www.scripps.edu/bashford).
It could be useful.
Best regards, Michal Otyepka
Received on Wed May 30 2001 - 04:50:10 PDT
