[gmx-users] pKa calculation from MD trajectories
David van der Spoel
spoel at xray.bmc.uu.se
Mon Apr 28 17:06:00 CEST 2003
On Mon, 2003-04-28 at 12:53, Peter Fojan wrote:
> 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.
And it should! That would be worth a paper I'd say. Is your program
available somewhere? How does it compare to MEAD?
> 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
> > SPIRITVS DVRISSIMA COQVIT
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Dr. David van der Spoel, Dept. of Cell & Mol. Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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