AMBER: identical high energies

From: Tanya Johannsen <>
Date: Thu, 17 Aug 2006 19:22:40 -0700 (PDT)

Dear AMBER community:

I am working with two slightly different conformations
of the same structure. I solvated each structure in
XLeap or TLeap and then subjected them to energy
minimizations. Something very strange happened: the
first energy of each run is extremely high, and this
first energy is identical between the two runs (even
though the components of the energy are different).
See below:

Conformation 1:
      1 1.0240E+16 1.5897E+15 6.9165E+17
    O 206760

 BOND = 16415.3128 ANGLE = 27628.7191
DIHED = 28244.3026
 VDWAALS = ************* EEL = -764301.4029
HBOND = 0.0000
 1-4 VDW = 16467.2056 1-4 EEL = 112089.5928
RESTRAINT = 0.0000

Conformation 2:
      1 1.0240E+16 1.5902E+15 6.9165E+17
    O 206646

 BOND = 9117.9973 ANGLE = 23174.0929
DIHED = 27422.7461
 VDWAALS = ************* EEL = -764246.3698
HBOND = 0.0000
 1-4 VDW = 15628.9916 1-4 EEL = 112229.3812
RESTRAINT = 0.0000

After this first step the energies for each structure
decrease in their own ways (no more equivalent
energies). The decrease in energy for the rest of the
run appears normal. However, I'm worried that this
first energy indicates some malfunction in the run;
could AMBER be giving this same high energy value when
overwhelmed by an energy that is too high?

The other question is why the energy would be so high.
I don't believe that the structure itself is the
problem, as it has already undergone a bit of
minimization in implicit solvent. In both cases the
offending atom appears to be a water molecule, but I
don't know why XLeap would have placed a water
molecule in such an unfavorable position. Does this
ever happen? I solvated using the solvateBox command,
and then added explicit salt with addIons2.

I would be very grateful for any suggestions. Thank
you in advance.


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Received on Sun Aug 20 2006 - 06:07:15 PDT
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