[gmx-users] DMSO, counter ions and ionization state
David van der Spoel
spoel at xray.bmc.uu.se
Fri Dec 3 13:46:00 CET 2004
On Fri, 2004-12-03 at 10:14 +0100, Edgar Luttmann wrote:
> Dear all,
> does anyone have experiences with the treatment of charges during
> peptide simulations in DMSO?
Long time ago we just did a simulation with a zwitterionic peptide in
DMSO, and lo and behold, it formed a stable saltbridge (Biophysical J.
72 pp. 2032-2041, 1997). As you say,it may not be correct.
> The pka of the sidechains as well as the termini might be significantly
> different in DMSO than 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
> Any suggestions are welcome and thanks in advance..
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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