AMBER: Questions

From: Joseph Fernandez <>
Date: Mon, 18 Sep 2006 11:48:25 -0700 (PDT)

I would be grateful for assitance on these questions:

1. I would like to rms fit frames from an MD
simulation to first frame of simulation with ptraj.
However, I need the water molecules to remain in the
same frame relative to the fitted structure. Is this
possible with ptraj?

2. Is it possible to carry out targeted molecular
dynamics using Poisson-Boltzmann solvation with water
cap with sander?


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Received on Wed Sep 20 2006 - 06:07:11 PDT
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