As an APBS user, I think it'd be useful to have the ability to readily calculate the pKa's in APBS.


Nathan Baker wrote:

Dear Sigrid --

What you describe is possible with APBS -- but not straightforward in
the current version.  You could use APBS together with PDB2PQR
( to protonate your system in various
titration states and then examine the changes in energy to determine the
intrinsic pKa's.  However, this is rather cumbersome and involves
several calculations.  We have plans to improve the ease of this
procedure in the near future.

In the meantime, I would recommend some of the tools that Jens Nielsen
(Cc'ed above) has developed for use with Delphi.  These offer a very
straightforward and robust way to calculate pKa's for proteins.  It may
also be possible to get Jens' tools to work with APBS; please let me
know if you would like to try.



Sigrid Gåseidnes wrote:

> Hi
> As a newbie in the field of electrostatics I am still very confused with
> all the different parameters, forcefields, gridsizes, charges etc. I
> have managed to install apbs and run some calculations, but I think it
> will take me quite some time before I really understand what the
> calculations do and how to interpret the results.
> What I would really like to do is to make my protein more stable at low
> pH, and to give me a hint of where to mutate I would like to calculate
> electrostatic potentials at different pH's. Is this possible in apbs? If
> not do you know another program where it is possible?
> Thanks
> Sigrid
> ********************************************
> Sigrid Gåseidnes
> Department of Chemistry and Biotechnology
> Agricultural University of Norway
> P.O.Box 5040
> 1432 Ås-NLH
> Norway
> E.mail:
> ********************************************
> _______________________________________________
> apbs-users mailing list

Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone:  (314) 362-2040, Fax:  (314) 362-0234

apbs-users mailing list

 This Mail Was Scanned By Mail-seCure System
 at the Tel-Aviv University CC.

Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university