[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 
> neutral?
> Any suggestions are welcome and thanks in advance..
> Edgar
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

More information about the gromacs.org_gmx-users mailing list