On Thu, Nov 8, 2012 at 5:55 PM, Pyle, Ronald <ronald.pyle.ttu.edu> wrote:
> 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.
>
EHBOND refers to a 10-12 potential that hasn't been used in the AMBER force
fields in many years. Unless you have good reason to suspect otherwise,
always assume this term will be 0.
ERESTRAINT is a measure of the restraint energy due to either 1) positional
restraints (when ntr=1) or 2) nmropt, flat-well restraints that can be
specified with nmropt=1 (but nmropt=1 can be used to specify things besides
restraints, too).
Therefore, if you have not set ntr=1 and you are not imposing distance,
angle, dihedral, or related restraints using nmropt=1, this is also fully
expected behavior.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Nov 08 2012 - 15:30:02 PST
