[gmx-users] pKa calculation from MD trajectories

Peter Fojan fp at bio.auc.dk
Mon Apr 28 12:45:01 CEST 2003

Dear Ivano,
we have developed a program called TITRA that can calculate the Pka
values of titratble residues in a protein. The input files would be the
structure of the protein. So basically this one could do it, but it
would be a bit tedious, becasue you would need snapshots from your
trajectory and process every single one with titra. But basically it can
be done.

Ivano Eberini wrote:

> Hi,
> we run some MD simulations for beta-lactoglobulin, starting from
> slightly different conditions.
> We were wondering if it is possible to calculate the pKa value for a
> specific residue (a glutamic acid) from MD trajectories.
> Thanks in advance for any suggestion and best regards,
> Ivano Eberini
> --
> Ivano Eberini
> Gruppo di Studio per la Proteomica e la Struttura delle Proteine
> Dipartimento di Scienze Farmacologiche
> Università degli Studi di Milano
> Via G. Balzaretti 9, 20133 - Milano
> tel.: +39-02-503-18304  fax: +39-02-503-18284
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