Re: [AMBER] Create EtOHbox

From: Mattei, Alessandra <>
Date: Fri, 4 Feb 2011 14:12:59 -0500

Thanks Francois for your suggestions.
I could solvate ethanol by itself and then equilibrate by MD to obtain the correct density.

Now I have another question. Once I did this, how can I solvate my organic molecule with the equilibrated ethanol box?

Alessandra Mattei
Department of Pharmaceutical Sciences
University of Kentucky
Lexington, KY 40536

From: FyD []
Sent: Wednesday, February 02, 2011 3:26 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Create EtOHbox

Dear Mattei,

> I would like to run a simulation of an organic molecule in ethanol.
> First I have to create an ethanol box, but in the amber library I
> could not find In addition, I think I need frcmod.etoh.
> I found tripos2.mol2 file and I should convert it to

For ethanol two conformations are possible; I would check if one or
two conformations where used in charge derivation. You can find mol2
files in R.E.DD.B.

Then you do not need to convert mol2 into off file, both are a format
of FF library (they have the same role).

> Could you please give me directions how to do that? Once I have
>, how can I create frcmod.etoh which contains parameters
> for ethanol in order to be able to solvate the molecule in ethanol?

You do not need any frcmod.etoh file because the required FF
parameters are in parm99.dat (or gaff.dat).

If the mol2 file comes from R.E.DD.B. you need to add the force field
atom types for the FF you decide to use, and then load the mol2 file
in LEaP & solvate ethanol by itself; save the prmtop/prmcrd files;
finally equilibrate by MD.
See for instance

regards, Francois

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Received on Fri Feb 04 2011 - 11:30:01 PST
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