On Thu, Apr 20, 2017, Manjula Saravanan wrote:
> I have done 50ns MD for my ligand-protein complex. I need to post
> minimize the MD trajectory in order to use it for the normal mode
> calculations. Kindly suggest me the minimization file format for post MD
> minimization. How to use it for normal mode calculations, Please help me
> out in this regard.
The mmpbsa_py scripts automate this procedure, and you look at the input files
it is creating. Basically, you need to strip waters and mobile counterions,
then minimize and run normal modes. See the mmpbsa_entropy.nab program
in $AMBERHOME/AmberTools/src/mmpbsa_py for details.
....dac
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Received on Thu Apr 20 2017 - 08:30:03 PDT
