From: prasun kumar (prasun30_at_gmail.com)
Date: Fri Jun 05 2009 - 02:51:37 CDT
I am trying to study protein-protein interaction using NAMD & CHARMM
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
10. I want to know whether I should "*tclforces on*" or not........
Thanx in advance
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