On Fri, Dec 05, 2014, 양지현 wrote:
>
> I try to run SANDER minimization using AMOEBA force field.
> When I compare TINKER and SANDER, their result don't match.
We need (lots) more information: how did you set up the Amber calculation?
What version of AmberTools and sander are you using? Which version of tinker?
Which version of the amoeba force field?
Do you mean that the results don't match at the beginning of the minimization
(with the same coordinates), or at the end of the minimization?
Can you compare individual components of the energy? Do any of these parts
match between the two programs?
With so many questions, I'm guessing that you will have to post files
for a small example that illustrates the problem.
It's also worth a quick test to see if pmemd.amoeba has the same problem.
Almost all Amber work with amoeba uses that program, rather than sander.
(Of course, we still need to find the solution, but it would narrow things
down to know if the problem is specific to sander or not.)
...thx...dac
>
> I referd to "http://biomol.bme.utexas.edu/wiki/index.php/Main_Page" for the calculation option.
You can also consult the files in $AMBERHOME/src/pmemd.amoeba/build_amoeba,
especially in the examples/JAC subdirectory. See if the exampels there match
what you are doing.
...thx...dac
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Received on Thu Dec 04 2014 - 19:00:02 PST
