Dear All, Hope this mail will find you in good health.
I am facing a problem regarding Position restrained dynamics (PR). I have done Molecular dynamic simulation (for cytosolic protein) but has not performed PR. So i m little confused if this effects the results and if yes to what extent it effects the outcome, Earlier, i performed PR as it is recomended but in my cases ,the generated structure was not correct as the core residues found to be reduced from 82%-52% and one bad contact was also observed. So i skipped the PR Step and run MD simultaion just after energy Minimization. I was wondering if PR is always necessary before molecular simulation without any exception. And if not, how can i justify this protocol that we have performed without PR. Or where i can find the references to justify the my protocol. Pawan Kumar Raghav Bioinformatician Stem Cell and Gene Therapy Research Group Division of Radiation Biosciences INMAS, DRDO Timarpur Delhi-110054 -- Pawan Kumar Raghav Bioinformatician Stem Cell and Gene Therapy Research Group Division of Radiation Biosciences INMAS, DRDO Timarpur Delhi-110054
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