[gmx-users] HIV protease dimer Energy minimization-ERROR

[serdar durdagi]

Dear Karunakaran,
   
  I don't think there is any error here.
   
  I have also made MD simulations of HIV-PR dimer with Gromacs, but I couldn't observed complete seperation of dimer to monomers. It seems after 1ns simulation, there is a seperation between tips of flaps. (I mean the seperation between Gly49, Ile50, Gly51 and Gly49', Ile50', Gly51').I measured about 5 Angstrom seperation (average), distance between the alpha carbon atoms for these residues after simulation. 
   
  When you put some inhibitors to this cavity, this seperation may restricted.
   
  You may check the article: Schuster et al, Biochemistry, 42, 1326, 2003.
   
   
  Serdar Durdagi
   
   
   
  

chandran karunakaran <ckaru2000 at yahoo.com> schrieb:
  Dear GMX users,

On running the MD for HIV protease as dimer
structure, it gets separated after the energy
minimization. (That’s dimer is separated into two
monomers). 

Could you kindly help me out in running HIV
protease as dimer? 

with thanks
c.karunakaran


*******************************+ 
Dr.Karunakaran Chandran +
Biophysics Department + 
Medical College of Wisconsin +
Milwaukee, WI-53226 +
Resi.: 414-443-0085 +
Off : 414-456-4034 +
********************************



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