thanks Christina :)
> Date: Tue, 19 Apr 2016 11:27:08 -0600
> From: cbergonzo.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] query about .mdcrd file
>
> 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.
> > > >
> > > > _______________________________________________
> > > > 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
> >
>
>
>
> --
> ---------------------------------------------------------------------------------------
> Christina Bergonzo, PhD
> Postdoctoral Researcher
> Department of Medicinal Chemistry, University of Utah
> http://home.chpc.utah.edu/~cheatham/
> ---------------------------------------------------------------------------------------
> _______________________________________________
> 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 Tue Apr 19 2016 - 23:30:03 PDT
