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Joined: Jun 2012
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As you can see in the subject line... This is the question... Previously, I have solvated ligands in water system using CHARMM GUI... For the current project, I want to solvate my ligand in ethanol...

What methodology should I follow to do this ???

Can you please give me an idea ???


Souparno Adhikary,


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Centre of Excellence in Bioinformatics,
Bose Institute,
Kolkata
Joined: Sep 2003
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rmv Online Content
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1) Build a box of solvent and equilibrate it.
2) Build the solute model, minimize in vacuum, possibly with restraints to preserve important structural features.
3) Combine systems, use DELETE with .AROUND. selection to remove solvent that overlaps the solute.
4) Minimize result, again probably with solute restraints.

There are examples in the Script Archive forum that can be adapted for the above steps using your specific system.


Rick Venable
computational chemist


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