On 4/14/13 2:13 AM, James Starlight wrote:
Dear Gromacs users!
I wounder to know if it possible to simple estimate drug affinity by mean
of MD simulation? As I know the drug's property is based on the free energy
change of bound-unbound ligand. So It seems that Justin's tutorial (free
energy calculations) might be usefull if it would not be so routine for the
drugs ( in that workflow several coulombic-vdw interactions must be
uncoupled). Is there any more easily way to perform such calculations for
the typical small-drug compounds consisted of several non-covalent
interactions with the receptors ?
Free energy calculations require considerable effort. You can approach the task
in a number of ways - FEP, BAR, TI, LIE, PMF, MM/PBSA, etc. There is a large
body of literature detailing methods for such calculations.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
