On Thu, 2014-05-08 at 23:30 +0530, MOHD HOMAIDUR RAHMAN wrote:
> Dear Amber Users
>
> I have three different types of molecules in my simulation box and each
> molecules have both Hydrogen bond donor and acceptor. Now I want to
> calculate Average Hydrogen bond number between each residue and Hydrogen
> bond energies per mole of solution. I went through AmberTool manual and I
> found information for Hydrogen bond number but I didn't found any helpful
> information about calculation of Hydrogen bond energies.
>
> Is any indirect way to calculate Hydrogen bond energies by using ptraj or
> ccptraj ?
No. Hydrogen bonds arise naturally from the electrostatic and van der
Waals interactions in the Amber force field.
Hydrogen bond occupancy and lifetimes may be of interest to you, though
(what percentage of time is the hydrogen bond 'present' and how long
does the hydrogen bond last before breaking at least temporarily,
respectively). You can compute these using cpptraj (the manual should
hopefully have sufficient detail to help you get started).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 08 2014 - 12:00:02 PDT
