[gmx-users] Reg : Protein-ligand complex using Amber force field

Justin A. Lemkul jalemkul at vt.edu
Sun Nov 27 22:42:53 CET 2011

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:


> 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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