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

From: David A Case <>
Date: Mon, 25 Feb 2019 11:07:47 -0500

On Mon, Feb 25, 2019, Prasanth G, Research Scholar wrote:

>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.

Thanks for your comments. I sympathize with the difficulty of
navigating through our list of tutorials, especially since many or most
of them deal with "advanced" topics, and those dealing with "basic"
simulations are all very old.

If you have a "standard" protein ligand complex, where the ligand is not
covalently bound to the protein, and the protein itself does not have
non-standard residues, then please look at this tutorial:

This walks you through a protein-ligand simulation. It ends with a
sander MD run. But the inputs for pmemd or pmemd.cuda are (almost)
identical to sander, so you can extend the run by switching from sander
to pmemd.cuda and continuing.

One note: characterizing (or even "observing") stability of a
protein-ligand complex is indeed an advanced topic, and you should
expect to have to think hard about how to proceed, whether in Gromacs or
Amber or whatever MD code you choose.

[Developers: we do need a "modern" update to this tutorial, and some
other basic (protein-only) tutorials that both actually work as written
for Amber18 pmemd, and which at least describe more realistic
calculations: current tutorials mostly have the disclaimer that "these
are not what you would really do, since we wanted users to get results
quickly". But we increasingly have actual scripts deposited as
supplementary material in recent publications: can we at create what
looks like a tutorial that points to one or more of them?

Second: it would be great to have a volunteer create a second "table of
contents" for the tutorials. The current list just says what is
covered, and really basic material like tutorial4b ends up near the
bottom of the list. A second toc could suggest tutorials or
combinations thereof, grouped by the type of problem addressed.]


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Received on Mon Feb 25 2019 - 08:30:02 PST
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