Re: [AMBER] Amber14 FEW for 3 trajectory free energy

From: Amy Rice <>
Date: Fri, 5 Aug 2016 10:21:50 -0500

Hi JoAnne,
Have you considered doing MMPBSA directly? My understanding is that FEW is
a workflow designed to automate the processing of multiple ligands bound to
the same receptor. In your case, it sounds like you have only one ligand of
interest and already have the three trajectories so I think might
be a better option. Take a look at tutorial A3 ( and the MMPBSA chapter of
the user manual to see what you think!

Hope this helps,
- Amy

On Fri, Aug 5, 2016 at 9:32 AM, JoAnne Babula <> wrote:

> Hello,
> I am currently using Amber14 on a Linux and am wondering if it is possible
> for me to use the FEW tool to calculate the binding free energy of a
> complex using the 3 trajectory method, but using my own previously
> generated simulations as opposed to generating them through the script as
> described in the very helpful tutorial A24 (
> advanced/tutorial24/#section1). I would like to use the script in Section
> 2
> of tutorial A24 to run GBSA analysis on 3 separate simulations (receptor,
> ligand, and complex) I have generated previously, but I am unsure how to
> specific that I would like these simulations to be used. I noticed the
> "trajectory_files" line in the mmpbsa_am1_3trj_pb0_gb2 input file has an
> automatically determined path. Is there any way I can alter this to direct
> the program to use my three separate trajectories instead? The receptor for
> this complex changes conformation when bound by ligand, so I would like to
> use the unbound receptor simulation to better estimate the binding free
> energy of the complex.
> Alternatively, if FEW is not capable of performing this calculation, is
> there a different tool in Amber that can?
> Thank you so much.
> --
> Very Respectfully,
> JoAnne J Babula
> IUSM Dept. of Pharmacology
> U.S. Army, 1LT, MS
> _______________________________________________
> AMBER mailing list

Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology
AMBER mailing list
Received on Fri Aug 05 2016 - 08:30:02 PDT
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