[gmx-users] pKa calculation from MD trajectories

[fp at bio.auc.dk]

>On Mon, 2003-04-28 at 12:53, Peter Fojan wrote:
Dear David,
the program is tested on a broad range of proteins and there are a number of
papers available on the electrostatic calculations on proteins including on
where this approach has been used to monitor the pk related changes on a peptide
during an MD run. The program performs actually very nice, I dont know about
MEAD but it has been tested against UHBD. The output from this program can be
used a input files for DELPHI and the charge distribution can be visualized
in GRASP.
The program is available from us for non profit organisations free of any charges.
The only thing to do is to fax us a signed license agreement and I deliver the
executables by email.
The only restriction so far is that it can only run under SGI IRIX. I still
have to port it to standard linux for a broader availability. It also has the
possibilities of taking measrued pKa values from NMR experiments and include
these in the calculation.
I hope this piece of information is useful,
Best,
    Peter
PS: I am working on a LINUX port of the program in my scare spare time. When
there is a release ready I will elt everybody who is interested know.

>> 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?
>
>> Best,
>>       Peter
>> 
>> 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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>-- 
>Groeten, David.
>________________________________________________________________________
>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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