Rohit Farmer wrote:
Dear GMX user,
Can anyone suggest how to use simulated a protein-ligand complex using
AMBER force field in GROMACS.
Though the force field is different, the workflow is the same as:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
And one thing more in another simulation i am trying to find out the
difference in protein complex interaction by mutating one residue. Right
now I am using simple procedure to perform simulation on the wild type
and the mutant complex. Is there any specific procedure which I can use
to record any significant difference in the complex just by the mutation
of one residue.
Conducting meaningful analysis implies you have some hypothesis to test and have
some biochemical knowledge of the system. There is no magic wand to wave to
parse out the answer. Some metrics may give you a general idea (RMSD, RMSF,
etc) but without a much more focused approach, you'll be stuck in the weeds.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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