Hi Matt,
yes it is straightforward to prepare mixed solvent boxes in amber as long as you know the concentrations you want and the prepi and frcmod parameters for those solvents.
You can also use Packmol (
http://m3g.iqm.unicamp.br/packmol/home.shtml) to define a fixed number of water + co solvent molecules you need for solvating your polymer of interest.
Thanks
Debarati
________________________________
From: Defrese, Matthew <matthew.defrese.uky.edu>
Sent: Tuesday, March 26, 2019 8:57 PM
To: amber.ambermd.org
Subject: [AMBER] Solvate with methanol and acetone using free energy methods?
Hello,
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 AMBER? We have seen that we can solvate with pure methanol, though not for acetone or their mixtures with water.
Is setting up and running free energy calculations in AMBER similar or equivalent to NAMD in terms of user friendliness?
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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Received on Tue Mar 26 2019 - 10:00:02 PDT
