Solvate with methanol and acetone using free energy methods in NAMD?

From: Defrese, Matthew (
Date: Sun Mar 24 2019 - 13:03:52 CDT


We are looking to model a system consisting of ligand binding to a synthetic polymer in varying solvent conditions such as water, acetone, methanol and their mixtures. Is there a straightforward way of solvating a box with these types of solvents in NAMD?

Is setting up and running free energy calculations in NAMD similar or equivalent to AMBER in terms of user friendliness? As all of our input files are in AMBER format, would there be any impediment to using these files in NAMD?

Thank you for any assistance,

- Matt Defrese

Graduate Student, Marsac Lab, Dept. of Pharmaceutical Sciences

College of Pharmacy, University of Kentucky

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