AMBER Archive (2006)

Subject: AMBER: Questions

From: Joseph Fernandez (
Date: Mon Sep 18 2006 - 13:48:25 CDT

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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