Hi Elvis,
Thanks for the help. I think i got it, it is running. Rest i will know
when final results come in.
Thanks again.
Regards
Abhilash
On Wed, Feb 1, 2017 at 5:59 PM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> 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
> > _______________________________________________
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Received on Thu Feb 02 2017 - 00:30:02 PST
