On Wed, Jun 07, 2017, Manjula Saravanan wrote:
> I have run 50ns MD for a ligand-protein complex. I need to
> calculate the entropy of binding for this complex. I want some help for
> preparing input files for normal mode calculation restricted around the
> residues in the active site (<10-12 angstroms). I have no idea about how to
> prepare the input files(all including nmode.in , .prmtop and .mdcrd) for
> this kind of nmode calculation. I kindly ask for help around here. I hope
> someone will give me a hand.
This sounds like a very non-standard calculation, so you may need to do some
experimentation. Something like this: use a reference frame to compute
which residues are within your cutoff (cpptraj can handle this); then use
that mask inside cpptraj to strip everything else away, and ask cpptraj
to create the stripped prmtop file at the same time. Then you should be in a
postion to run quasi-harmonic or normal mode calculations in the usual way.
I'm not sure what sort of accuracy you should expect. You might want to
experiment with different sizes of region around the active site to see
how sensitive entropy changes upon ligand binding are to size.
...hope this helps...dac
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Received on Thu Jun 08 2017 - 06:00:05 PDT
