> Can someone please provide some guidance, I am new at AMBER and running
> MD simulations on a ssDNA 10mer. I have read everything I can find to
> determine why my mdout file does not provide values for EHBOND and
> RESTRAINT. I assume it involves the parameters I set up, but after
> changing several, turning off SHAKE and extensive reading, nothing I do
> is providing a value for either of these forces.
Most of the AMBER force fields do not have explicit terms for hydrogen
bonds other than what is obtained from a combination of electrostatics and
van der Waals interactions. There is a old paper from the Kollman lab (J
Comp Chem 12, 620-626 (1991)) that explains the move away from an
additional and explicit hydrogen bond term (10-12) [that is reported in
the EHBOND value] to regular electrostatics and van der Waals. In other
words, the point charges lead to a dipole such that electrostatics can
model the dipole-dipole interaction to some degree.
With respect to restraint energy, you will only have this if you add in
restraints (for example positional restraints with NTR=1). [Note that
SHAKE is not a "restraint" but a constraint.]
--tec3
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 08 2012 - 15:30:03 PST
