Hi
Thanks for the reply. I had a look at the FEW work flow it seems to be a
streamlined flow of doing Free energy calculations using different
techniques. I went through its nicely written tutorial. I think i will use
it in my other studies.
But in my case all seven ligands (same ligand different binding pockets)
are simultaneously bound to the protein in a single trajectory and i need
to estimate the Free energy of each ligand one by one. I cannot separate
each ligand and run a individual simulation as it will cause a unrealistic
conformational change. All ligands must be present simultaneously as in the
wet lab experimental studies.
I could not find how could FEW workflow be changed to suit my needs. I
might have missed something, in which case please let me know.
Regards
Abhilash
On Wed, Feb 1, 2017 at 8:43 AM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> See this tutorial http://ambermd.org/tutorials/advanced/tutorial24/ its
> on Free energy workflow. It might be helpful
>
> [http://ambermd.org/tutorials/advanced/tutorial24/figures/Table1.gif]<
> http://ambermd.org/tutorials/advanced/tutorial24/>
>
> Amber Tutorial A24 - FEW<http://ambermd.org/tutorials/advanced/tutorial24/
> >
> ambermd.org
> Figure 1: Schematic depiction of setup of MD simulations with FEW. Input
> information used in this tutorial is highlighted in blue, input data that
> may be required for ...
>
>
>
>
> Best Regards
>
> [photo]
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
>
>
> [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> in/elvisadrianmartis/>
>
>
>
>
>
> ________________________________
> From: Abhilash J <md.scfbio.gmail.com>
> Sent: 31 January 2017 21:50:05
> To: AMBER Mailing List
> Subject: [AMBER] Multiple ligands in MMGBSA
>
> Hi everyone!
>
> I want to run MM GBSA on a trajectory. My complex has 7 ligands. All
> ligands are identical but at different positions. They have different
> residue numbers. How can i calculate the MMGBSA energy for a specific
> ligand residue.
> Is it possible to calculate MMGBSA energy for all ligands in a single run
> of MMGBSA.
>
>
> Regards
>
> Abhilash
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Received on Wed Feb 01 2017 - 03:00:02 PST
