[AMBER] want to keep water from the pdb

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Tue, 15 Jun 2010 12:20:03 +0530

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?

And how do I keep track of them during the simulation?

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

How do I find their contribution to the Delta G when I perform MMPBSA
analysis using MMPBSA.py?

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
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Received on Tue Jun 15 2010 - 00:00:04 PDT
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