[gmx-users] ligand energy calculation PME simulation

Mark Abraham Mark.Abraham at anu.edu.au
Tue Sep 8 04:19:00 CEST 2009

Antonio Coluccia wrote:
> Hi All
> I have  problems with the binding energy. I have done a series of dynamics simulation on a series of analogues compounds using PME and i would like to compute the binding energy of all the analyzed compounds.
> I have read a lot on the mail archive but it is still unclear. I have done a dynamics of the complex (protein+ligand) and I repeated the same analysis for the ligand in solution. I am not using g_lie since I used PME. I'm using the aveage values for Coul and LJ energy but the resulting binding energy is not real. What I have to do to avoid PME contribution. I am doing same mistakes ?

Either avoid using PME, or do a real free energy calculation (which will 
only be feasible for a very small ligand), or do an implicit solvation 
estimate using (e.g.) APBS.


> Could someone help me please? Any idea will be really appreciated.
> Ant.
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list