[gmx-users] Re:How to define the protonated state of a protein

Xavier Periole x.periole at chem.rug.nl
Fri Oct 29 10:47:51 CEST 2004

PeiQuan Chen wrote:

>Dear gmx-users,
>>The protonation state for a residue in a particular protein may be 
>>different from the residue's protonation state in solution, so to be more 
>>confident you have it right you need to do a pK calculation, which takes 
>>into account other charges in the protein and the fact that the bulk of the 
>>protein has different dielectric properties from electrolyte.	
>Thank you for Eric respond. Does anybody have experience in pKa calculation? 
>Do you mind telling me which software which is free to obtain to do these Job?
Different softwares are available, and different method are used by
people. To my
knowledge the faster way to get them is the program MMC from Mehler. You can
ask him to get a version of it and conpile it. I used it for different
proteins and the
results are quite reasonable.

Mehler email: elm2020 at med.cornell.edu>

web page: http://fulcrum.physbio.mssm.edu/~mehler/



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

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