hi... we're running some dynamics for a dna molecule with a carcinogen. the
structure is very flexible during the dynamics, and we want to calculate the
free energy of it. for entropy calculation, is it better to choose several
structures from the dynamics, and estimate the entropy of it using nmode
after minimization. also for energy calculation using mm_pbsa, we found that
the standard deviation of the free energy is kind of large, which is also
due to the flexibility of the structures. we're concerning if the final
results are still reliable due to the big standard deviation. thanks a
lot... frank
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Received on Tue Apr 11 2000 - 10:42:28 PDT
