Dear Amber community members and Jason,
Thanks a lot for those suggestions and inputs.
On Tue, Jun 15, 2010 at 12:30 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> On Tue, Jun 15, 2010 at 2:50 AM, vaibhav dixit <vaibhavadixit.gmail.com
> >wrote:
>
> > Dear Amber community members,
> > Thanks for your suggestions earlier.
> > I'm studying 2PRG.pdb complex by 1ns MD simulations.
> > I want to evaluate the importance of some water molecules in the pdb.
> >
> > How do I make sure that the water molecules from the original pdb are
> > retained during the prmtop and inpcrd file generation?
> >
>
> You do this by NOT removing those water molecules from the PDB before
> creating the topology file. Any waters you keep in the PDB will be made
> part of the solvent in the prmtop. Moreover, they will be the first
> waters,
> appearing in the order they appeared in in the PDB file (I'm pretty sure).
> You can check this with a visualization program such as VMD.
>
>
> >
> > And how do I keep track of them during the simulation?
> >
>
> Water molecules do not change places within the topology file throughout
> the
> course of the simulation. However, the water molecules will almost
> certainly exchange, so the waters that were in the bridge to begin will not
> necessarily be part of the bridge throughout the entire course of your
> simulation. To get this, see the "closest" command in ptraj. It is
> described in the manual.
>
>
> >
> > There are 8642 water molecules added by tleap. Please find time and see
> if
> > you can suggest me some tool where I can keep track of these water
> > molecules.
> >
>
> With VMD, you can label a water and track its movement during a simulation.
> You can also measure the distance between 2 atoms (for instance, the O in
> a
> water molecule and the CA of an amino acid of interest) and easily plot
> that
> distance profile as a function of the simulation. However, it may not be
> very interesting, since once it leaves the bridge, it seems to me that you
> would merely be measuring diffusion.
>
>
> >
> > How do I find their contribution to the Delta G when I perform MMPBSA
> > analysis using MMPBSA.py?
> >
>
> You have to prepare the coordinate file yourself using the "closest"
> command
> in ptraj to keep a specified number of waters. Then, don't forget to keep
> that number of waters in your complex and receptor prmtop files, and use
> strip_mdcrd=0 in the input file (make sure you are using the latest version
> of MMPBSA.py for this, downloadable on the MMPBSA tutorial website).
>
> Good luck!
> Jason
>
>
> >
> > Waiting for you comments and suggestions...
> > --
> > With regards
> >
> > Vaibhav A. Dixit
> > Ph.D. Scholar
> > Department of Medicinal Chemistry
> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> > Punjab -160 062 INDIA
> > Phone (Mobile): +919915214408
> > E-mail: vaibhavadixit.gmail.com
> > www.niper.nic.in
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Tue Jun 15 2010 - 03:00:05 PDT
