Re: [AMBER] want to keep water from the pdb

From: Jason Swails <>
Date: Tue, 15 Jun 2010 03:00:44 -0400


On Tue, Jun 15, 2010 at 2:50 AM, vaibhav dixit <>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

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 for this, downloadable on the MMPBSA tutorial website).

Good luck!

> 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:
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Jun 15 2010 - 00:30:03 PDT
Custom Search