[gmx-users] pH

Marco Ceruso mceruso at physbio.mssm.edu
Tue Aug 12 22:12:01 CEST 2003

check out this webpage:
there is a link to a method that predict pKa values of aa in proteins. There
are other methods, as well. There was a discussion about some of them in the
list a few months ago.
In any case once you have determined the pKa of your titrable groups you
will assign the corresponding protonation state accordingly.
If you don't want to run a pKa calculation some standard values of pKa are
given in biochemistry text books, but you should be aware that e.g. the pKa
of buried titratble aa may deviate significantly from these standards

-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Osmany Guirola Cruz
Sent: Tuesday, August 12, 2003 3:41 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] pH

Two questions.I have my system(for example a peptide in a box of water)
How can I calculate the pH of the sysytem and
How can I do a simulation of this system whith a given pH.
For example I want a simulation of the system whith pH=4 and another

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