Dear Amber Users:
I know a single water molecule shouldn't have the nonbond interactions. I am surprised to see sander will calculates the electrostatic for a single TIP3P water molecule simply if the bond between hydrogen atoms is removed. What I did is as follows:
--------- In Leap ----------------------------------------------------
source leaprc.ff99SB
w=copy WAT
deletebond w.1.H1 w.1.H2
saveamberparm w w.top w.crd
---------------------------------------------------------------------
The sander output is as follows:
---------------------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 3.8140E+01 1.1876E+01 1.9923E+01 H2 3
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
VDWAALS = 0.0000 EEL = 38.1400 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
----------------------------------------------------------------------------------------------------
The electrostatic energy for single water molecule with H-H bond removed is 38kcal/mol !
Am I doing something wrong? Any help is highly appreciated!
Jinfeng
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 14 2014 - 08:30:02 PDT
