RE: Calc. of pKa and total charge??

Dear Mathias,
 You may be interested in ACD/pKa predictions, which will calculate
 pKa in one of three selected modes.
 The ?apparent constant? of the pKa is a method of calculation which
 mimics the experimental situation by ?adding? protons to the molecule
 in the order the molecule would normally be protonated in solution.
 The ?microconstants of current form? is a method of calculation which
 accepts the input structure exactly as it is, and tries to remove a
 proton from it.
 The "single pKa" is a method intuitive to the way medicinal chemists
 view
 pKa values.  If there are two acidic sites in the molecule, a chemist
 desires to know the relative acid pKa values.  It could be done by
 calculating the pKa for each ionization site while the rest of the
 molecule is considered neutral.  This is not what actually happens
 experimentally, if a di-acid is dissolved in strong base and titrated
 with acid, but it does indicate the relative ease of ionization at each
 center.
 If you would like to trial these methods, please visit our online
 interactive laboratory, www.acdlabs.com/ilab , or you may email
 me a structure, and I can do a prediction for you.  You may also
 contact one of our representatives at sales-0at0-acdlabs.com .
 You may use our freeware ChemSketch 4.5 interface to connect
 to the interactive lab, by downloading at www.acdlabs.com/download ,
 or simply use the JAVA structure drawing applet at the ILAB web
 site.
 Best wishes,
 Gavin Shear
 -----Original Message-----
 From: Computational Chemistry List [mailto:chemistry-request-0at0-ccl.net]On
 Behalf Of Mathias.Norrman-0at0-eu.apbiotech.com
 Sent: Tuesday, July 25, 2000 5:07 AM
 To: chemistry-0at0-ccl.net
 Subject: CCL:Calc. of pKa and total charge??
 *** (Sorry for sending a second copy of this but this one has a correction
 of my email adress.) ***
 Hi,
 I would like to calculate pKa of individual residues within a protein in
 order to get the total charge as a function of pH. As far as I understand
 the pKa is dependent to some extent on the local micro environment. I
 wonder if there is a program that calculates pKa of individual residues in
 a position specific manner.
 With this information I think it´s possible to calculate charges of the
 residues and the protein in total as a function of pH.
 Perhaps someone knows a program that can do any of this or help me with a
 description of how to proceed.
 I have DelPhi available but any other program is of interest.
 Thanks in advance!
 /Mathias Norrman
 mathias.a.norrman-0at0-eu.apbiotech.com
 Amersham Pharmacia Biotech
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