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

From: Gustaf Olsson <>
Date: Thu, 12 Sep 2019 05:38:18 +0000

I once threw together a “flowchart” and recently dug this up to present during a workshop:

It is not made with peptide/protein/ligand simulations in mind but rather “small-molecule-solutions-simulations” (don’t know if that makes sense). Even though all steps most likely won’t be necessary (like Avogadro structure drawing and minimisation) and some of the “input” examples (as i noticed during the presentation) are now very outdated, you should be able to use it to piece together a workflow together with the tutorials.

Just keep in mind, my settings are most likely not exactly what you want and there is a 100% chance that there is something wrong with at least one thing I have not noticed yet.

Good luck and best regards
// Gustaf

On 12 Sep 2019, at 00:06, Renato Araujo <<>> wrote:

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 Amber18.
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.

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 Wed Sep 11 2019 - 23:00:02 PDT
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