regarding protein-protein interaction

From: prasun kumar (prasun30_at_gmail.com)
Date: Fri Jun 05 2009 - 02:51:37 CDT

Dear all

I am trying to study protein-protein interaction using NAMD & CHARMM
forcefield.

Steps I am following are:

   1. two proteins are placed at a distance of 10 angstrom to each other
   2. minimized in vacuum
   3. solvated in water and ionized
   4. Minimization was done again
   5. I have done the equlibration also
   6. while doing dynamics ,volume is getting decreased and at last
   simulation is stopped saying fatal error related to the volume and asking to
   increase the margin.
   7. what should I do for it????????
   8. I have studied that two proteins are interacting to each other(its
   proved in wetlab)
   9. while doing dynamics the two proteins are not seems to coming towards
   each other
   10. I want to know whether I should "*tclforces on*" or not........

Thanx in advance
with regards
Prasun kumar

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