On 5/28/12 7:07 AM, Kowsar Bagherzadeh wrote:
Dear users,
I have done a Ligand-Protein Simulation using 43a1.ff forcefield and
ssDNA-Protein (the same protein I used for ligand protein simulation) using
amber99sd-ILDN forcefield. Is it possible to compare the results of the two
simulation with eachother? No?
Maybe it's possible, but there will be a lot of caveats to the results. You may
know of some intrinsic limitations or benefits of each force field that may
explain away discrepancies, but the real complication comes with the ligand.
How did you generate its parameters? Do you know exactly how those parameters
will affect the local dynamics of the residues in which it makes contact? Do
you know the equivalent result using a suitable Amber force field? If the
answer to any of these questions is no, you'll have a hard time convincing a
reviewer that your comparison is very meaningful.
Net result: choose a force field, and use it for all simulations you wish to
compare. It is substantially easier than trying to wiggle your way into a
potentially incomplete or incorrect interpretation of the results.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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