You can start by taking a look into Chapter 10 of the Amber15 manual, that you can find here:
http://ambermd.org/doc12/Amber15.pdf
There you will find details on the calculations, as well as some example files.
Gustavo Seabra
> Em 23 de nov de 2015, à(s) 10:15, Sivanandam M <sivanandamphy.gmail.com> escreveu:
>
> Respected sir,
> I have a protein-ligand complex inwhich protein has
> 317 amino acids and ligand has 51 atoms. i am trying to do QM/MM
> calculation. In this calculation, i have to fix the QM region of that
> ligand with interactions. If anyone help me, how to accurately fix the
> dimension of the QM region, and advice me which software can be use to
> visualize the QM region box.
>
> Thanks in advance
>
> --------------------------------------------------------
> M.SIVANANDAM
> Research Scholar
> Department of Physics
> School of Physical Sciences
> Periyar University
> Salem-636 011
> Mobile- 9965582730, 9042066076
> --------------------------------------------------------
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Received on Mon Nov 23 2015 - 06:30:03 PST
