Hi Amy,
I have taken a look at tutorial A3, and I don't think it's quite able to
calculate what I need. Do you know if MMPBSA is capable of calculating the
total free energy of the ligand alone without water? I have a simulation of
the ligand by itself, no receptor or protein, and I would like to use that
to calculate the free energy for the ligand.
On Fri, Aug 5, 2016 at 11:21 AM, Amy Rice <arice3.hawk.iit.edu> wrote:
> 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 MMPBSA.py might
> be a better option. Take a look at tutorial A3 (
> http://ambermd.org/tutorials/advanced/tutorial3/) 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 <jbabula.umail.iu.edu>
> 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 (
> http://ambermd.org/tutorials/
> > 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Amy Rice
> Ph.D. Student
> Physics Department
> Illinois Institute of Technology
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Very Respectfully,
JoAnne J Babula
Ph.D. Candidate, IUSM, Dept. of Pharmacology
U.S. Army, 1LT, MS
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Received on Tue Aug 09 2016 - 11:30:02 PDT
