[AMBER] Protein-ligand simulation and help w.r.t files for carrying out simulation

From: Prasanth G, Research Scholar <prasanthghanta.sssihl.edu.in>
Date: Mon, 25 Feb 2019 18:23:34 +0530

Dear all,
I am interested in running a 30ns simulation of a protein-ligand complex to
observe the stability of the same.
I am relatively new to AMBER and having difficulty in finding a proper
tutorial for latest version of Amber (amber 17 and above with pmemd.cuda).
As i understand,
we need to prepare the ligand and protein co-ordinate and topology files
(using ambpdb, pdb4amber and antechamber). After which, we need to obtain
the same for the complex.
Coming from Gromacs, I have a rough idea of the energyminimization,
Equilibration with (nvt, npt) during which restraints are placed on the
ligand and protein.
This will be followed by MDrun.
After looking at the various tutorials for amber, I am thoroughly confused.
It would be of great help, if someone could point me in the right direction
or share the work flow for the simulation.

Thank you,

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Received on Mon Feb 25 2019 - 05:00:01 PST
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