On 28/07/2012 4:49 PM, Rajitha Tatikonda wrote:
Hi,
I am intending to calculate binding affinity using Linear Interaction
method (LIE method) for which I need to perform two simulations for
given ligand both in free and bound states and get the values of
Electrostatic and Van der Waals Interaction energies of the ligand.
I have done simulation of free state of ligand. As Peptide (Chain C)
of complex is the ligand, I could not understand how this is to be
specified under energy-grps option in mdp for my system (as it is done
in protein -ligand complex gromacs tutorial by specifying protein,
JZ4(name of the ligand)).
So the
http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups
won't be suitable and you'll have to make some custom groups in your
http://www.gromacs.org/Documentation/File_Formats/Index_File
Mark
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* 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
