Re: [AMBER] tLeap and acetonitrile/chloroform solvation

From: David Case <>
Date: Wed, 4 Jan 2017 21:51:18 -0500

On Wed, Jan 04, 2017, Luka Bilić wrote:
> I am writing to enquire about solvation of organic molecules in Amber 16.

First, you need to make a molecular mechanics description of a single solvent
molecule. This is no different from making files for any organic molecule:
antechamber is probably the most widely-used package, but R.E.D. or a search
engine (I use Google myself, but other search engines exist) are good
alternate approaches.

Once you have files (e.g. mol2 and frcmod) for a *single* solvent molecule,
you need to use that molecule as a solvent.

> How do I use "solvateoct molecule Solvent 14.0" correctly?
> Do I have to have chloroform structure minimized (in Gaussian for
> instance) and then turned into .mol2 file, after which I load it in
> tLeap using "Solvent=loadmol2 Solvent.mol2" or do I have to do
> something else?

What you describe above is the traditional "tleap" approach. This ought to
work, and you don't say what happened when you tried that.

However, I'd strongly recommend an alternate approach: use packmol (not in
Amber) or AddToBox (comes with AmberTools) to create a pdb file with you
solute atom and the desired number of solvent molecules. Then use loadPdb
to load that file into tleap. No need for solvateBox or solvateOct: just
use "set unit box..." to establish the periodic box.

> 2nd question/problem
> Since I have found no acetonitrile .lib files. How do I make a solvent
> box containing well defined .frcmod and .lib files. My current .frcmod
> files made from Acetonitrile.mol2 all end up empty.

This is (probably) fine. You don't say exactly what you did, but all the
parameters needed for acetonitrile are already in gaff.dat (or gaff2.dat)
and having an empty frcmod file is OK (you can just delete it.)


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Received on Wed Jan 04 2017 - 19:00:02 PST
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