Re: [AMBER] tLeap and acetonitrile/chloroform solvation

From: Luka Bilić <>
Date: Thu, 05 Jan 2017 09:09:41 +0100

Thank you for your reply!
This was most helpful!

I did try some of these things before (the traditional tLeap approach)
and some worked the way I assumed it will, but now I have confirmation
from you that I was aiming in the right direction.

By using openbabel software I was able to get "real" .mol2 extension
from G09 .log file. Then .frcmod contained some variables. But for now
I will go step by step and learn.

Once more, thank you!

Yours Luka

Citiram David Case <>:

> 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.)
> ....dac
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Received on Thu Jan 05 2017 - 00:30:03 PST
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