Hi,
In MMGBSA analysis what you do (most of the time) is run a simulation which
is water+protein+ligand (for example). Then, you use the script mmpbsa.py/pl
to find the binding free energy from the thermodynamic cycle (first page of
the tutorial).
To do this, you take the trajectory you just ran (the single .mdcrd file)
and split it up based on the parmtops (complex without water, ligand only,
protein only, and entire system), and the script calculates the binding
free energy for each frame of the trajectory, and then probably gives you
an average.
You shouldn't have individual trajectories for each topology, unless you're
doing something different.
Hope this helps,
Christina
On Tue, Apr 19, 2016 at 11:12 AM, Ayesha Kanwal <ayesha_comsian.hotmail.com>
wrote:
> Hi,
> i know prmtop files are topology files and mdcrd files are trajectory
> files. But may be i am not successful to ask the actual thing which i want
> to know :( .
> i have confusion in that thing how many trajectory files would it cover ?
> is this command need all the trajectory files of all these four topolgy
> files or something else. hope so you can understand my confusion.
>
> > From: mohammad.shahid.gmail.com
> > Date: Tue, 19 Apr 2016 14:48:20 +0200
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] query about .mdcrd file
> >
> > Hi,
> >
> > I think you were confusing the prmtop and mdcrd files. The solvated files
> > for complex, receptor and ligand are the topology files, while the
> *.mdcrd
> > are the trajectory files.
> > The same topology files can be used for all of the trajectory files.
> > Hope it clears the confusion now?
> >
> > Best regards,
> >
> > --
> > Shahid.
> >
> >
> > On Tue, Apr 19, 2016 at 1:23 PM, Ayesha Kanwal <
> ayesha_comsian.hotmail.com>
> > wrote:
> >
> > > Hi all ,
> > > i wan to know in amber advanced tutorial for the calculation of
> > > MMPBSA/GBSA.
> > > we take (-y *.mdcrd) it means we take that files that starts with
> .mdcrd
> > > extension
> > > it means it take all 4 mdcrd files of solvated complex,complex,
> receptor
> > > and ligand.
> > > then how system can detect which mdcrd file is for solvated complex and
> > > semoltaneously.
> > > can any one clear my concept.
> > >
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> > >
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--
---------------------------------------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
http://home.chpc.utah.edu/~cheatham/
---------------------------------------------------------------------------------------
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Received on Tue Apr 19 2016 - 10:30:06 PDT
