[MMTK] Errors in energy evaluation with mg ion

Ryan Gutenkunst rng7 at cornell.edu
Tue Jul 20 22:38:01 CEST 2004


Eric Zollars wrote:
 > Ryan-
 > A quick look at your errors suggests that the energy evaluator is
 > looking for the Lennard-Jones parameters.  I could be wrong, but check
 > out the argon entry in Database/Atoms/ar for comparison.
 > Good luck.
 > Eric

Eric,

Thanks for the suggestion, but as a check I appended the following lines 
from the Atoms/ar to my Atoms/mg and I still get the same error.

LJ_radius = 3.4*Ang
LJ_energy = 120*K*k_B

b_coherent = 1.909*fm
b_incoherent = 0.*fm
b_coherent_deut = 1.909*fm
b_incoherent_deut = 0.*fm

I hope I don't need to go mucking with the Amber files. Does anyone else 
have ideas?

Ryan

> Ryan Gutenkunst wrote:
> 
>> Hi all,
>>
>> I'm trying to simulate a protein along with a magnesium ion present in 
>> the pdb file, and I'm getting errors in the energy evaluation.
>>
>> Below I've attached the traceback, and my Database files Atoms/mg and 
>> Molecules/mg
>>
>> Does anyone know what's wrong?
>>
>> Thanks for any help,
>>
>> The traceback is here:

<snip>

-- 
Ryan Gutenkunst               |
Cornell Dept. of Physics      |       "It is not the mountain
                               |        we conquer but ourselves."
Clark 535 / (607)255-6068     |        -- Sir Edmund Hillary
AIM: JepettoRNG               |
          http://www.physics.cornell.edu/~rgutenkunst/




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