> If so, in order for a comparable number to emerge from quasih-harmonic
> analysis, I believe you will need to run three lengthy trajectories, one for
> each of receptor, complex, and ligand. Then, you perform ptraj on these
> separate trajectories.
...
> > of TdS = T ( S(complex) - S(receptor) - S(ligand)). Here S is the
> > total entropy from the output of ptraj.
> > trajin ./md_prod.mdcrd 1000 5000 1
> > rms first .CA,C,N
> > matrix mwcovar name com-var :1-131,132
> > analyze matrix com-var out com-cov thermo reduce
> > matrix mwcovar name rec-var :1-131
> > analyze matrix rec-var out rec-cov thermo reduce
> > matrix mwcovar name lig-var :132
> > analyze matrix lig-var out lig-cov thermo reduce
Alternatively, if you do not run each trajectory independently, you will
likely have to separately fit each sub-region before calculating the
entropy otherwise it will include additional degrees of freedom, i.e. be
fluctuating not about its sub-structure average but about the full complex
average. I would separately fit each region before doing the entropy.
reference avg.pdb pdb
rms mass reference :1-132
matrix mwcovar name com-var :1-132
analyze matrix com-var out com-cov thermo reduce
rms mass reference :132
matrix mwcovar name lig-var :132
analyze matrix lig-var out lig-cov thermo reduce
Note also that the entropy values obtained will depend on the number of
frames and also be biased by sub-state crossing (leading to larger
entropies) if you are moving among sub-states in the MD.
For the length dependence, see Harris et al, JACS ~2001 and BJ ~2005.
-tec3
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Received on Sun Apr 22 2007 - 06:07:33 PDT
