THANKS to both tec3 and Jason for the explanations. Good to know that I have done nothing "wrong" and that this is not an "error" in my simulation.
So, if I want to know about the H-bonds, the archives provide direction to go to a specific tutorial. Which I did and found very helpful guidance for H-bond analysis for proteins. Is there a tutorial for H-Bond analysis for DNA or has someone on the list used the H-bond analysis for DNA; that wouldn't mind providing some guidance and/or scripts??
Thanks
Ron
________________________________________
From: tec3.utah.edu [tec3.utah.edu]
Sent: Thursday, November 08, 2012 5:25 PM
To: AMBER Mailing List
Subject: Re: [AMBER] EHBOND values and RESTRAINT values in mdout file
> 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
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Received on Fri Nov 09 2012 - 06:30:02 PST
