Hi,
In that case what you can try is treat the other six ligands as part of the receptor while you compute the free energy of one of the ligands. This way you will need to run your MM-PB(GB)SA 7 times, once for each ligand.
Perhaps, someone on this list will have a better solution.
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Abhilash J [mailto:md.scfbio.gmail.com]
Sent: Wednesday, February 01, 2017 4:09 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Multiple ligands in MMGBSA
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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 01 2017 - 05:00:02 PST
