Dear AMBER User's
I want to calculate hydrogen bond energy between pairs of 500 water
molecules.
In old Amber Force Field contained Hbond term ( J . Amer. Chem. SOC.,
106,765 (1984) & Journal of Computational Chemistry, Vol. 7, No. 2, 230-252
(1986)), that represents 12-10 potentials function as sum [Cij / Rij^12 -
Dij / Rij^10]. The reported parameter of C and D are 7557 and 2385
respectively.
Now I have following question:
1) Would I used the same FF formula for H-bond energy calculation by taking
same C and D parameter for donor and acceptor in water?
2) The distance Rij are neighbour atoms distance or all interacting pairs
distance.
3) Would I used cpptraj to calculate Rij or hbond energy ?
4) Would I also consider the lone pair on oxygen because during Hbond
calculation in AmberTool, Cpptraj consider lone pair on oxygen?
Thank you in advance for your reply or any suggestion.
Regards
Rahman
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
*M*d* H*omaidur* R**ahman *( Research Scholar )
Lab No. 510, Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036, India
*Mobile No = +91- 7845991785*
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 25 2018 - 08:00:03 PST
