Subject: CCL: DMSO, counter ions and ionization state

From: Edgar Luttmann <edgar.luttmann(at)mpi-bpc.mpg.de>
Date: Fri, 03 Dec 2004 10:21:44 +0100

Dear all,

does anyone have experiences with the treatment of charges during 
peptide MD simulations (with gromacs) in DMSO?

The pka of the sidechains as well as the termini might be significantly 
different in DMSO compared to water and thus I wonder if there is a 
convenient way to estimate the ionization state of the residues. 
Furthermore would you just put counter ions into the DMSO - or would you 
keep the peptide neutral?

Any suggestions are welcome and thanks in advance..

Edgar

-- 
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Dr. Edgar Luttmann
Max-Planck-Institute for Biophysical Chemistry
Department 070 - Theoretical and Computational Biophysics Group

Am Fassberg 11, 37077 Goettingen, Germany
Tel: +49 551 201-2320, Fax: +49 551 201-2302
E-Mail: edgar.luttmann( at )mpi-bpc.mpg.de / eluttma( at )gwdg.de
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