Hi Gideon, If the binding is relatively weak and the force field parameters are good enough that should be feasible. See e.g., Biophys J. 2005 August; 89(2): 768–781. However, in other cases this is more challenging. This is discussed in details for simulations of a Zinc binding protein in Phys Chem Chem Phys. 2009 Feb 14; 11(6): 975-83
Good luck, Ran ------------------------------------------------ Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden +46 480 446 290 Telephone +46 76 207 8763 Mobile [email protected] http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en ------------------------------------------------ ________________________________________ From: [email protected] [[email protected]] On Behalf Of גדעון לפידות [[email protected]] Sent: 30 November 2010 10:45 To: [email protected] Subject: [gmx-users] Claculating Equilibrium constants Hello all, I have a protein bound to ions. is there a way to calculate the Kd of the bound ion in Gromaces so I can compare it to experimental Kd? Thanks, Gideon
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
