Re: [AMBER] Using a box of organic solvent

From: David A Case <>
Date: Fri, 31 May 2019 08:14:51 -0400

On Fri, May 31, 2019, Alessandro LANDI wrote:
>Starting from a pdb file retrieved from the "ATB" repository and using
>the Packmol software, I have been able to build a cubic box of 500 THF
>molecules. I have also evaluated the RESP charges and all the parameters
>needed in AMBER for that solvent, by using ANTECHAMBER suite.
>My question is: in order to use THF as an explicit solvent in AMBER
>simulations, which files do I have to use and in which folder do I need to
>put them?
>Finally, which commands do I need to use in Leap, (maybe via "solvateoct"?)
>to use this THF box I have built?

If you are familiar with packmol, I'd suggest using that program to
build your solute/THF solvent box, saving it as a PDB file.

Then, in tleap, load whatever force field you need for the solute; load
the unit for THF and its frcmod file; then use loadPdb to load the PDB
file that packmol created.

The "solvateoct" and "solvatebox" commands work fine for a small solvent
like water, but are less well suited for organic solvents, where each
solvent molecule is much bigger.

If you follow this path, you won't actually need the box of 500 THF
molecules you made, but the packmol experience you gained by doing that
should serve you in good stead: just use packmol to create the actual
system you want to simulate.

Others may have different preferences. As an aside, note that packmol
is now included with AmberTools19, so there is no separate software to


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Received on Fri May 31 2019 - 05:30:02 PDT
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