Re: [AMBER] solvation of a pdb file

From: David A Case <>
Date: Sun, 19 Oct 2014 13:47:46 -0400

On Sun, Oct 19, 2014, Robin Jain wrote:
> I have a organic molecule and i want to simulate in a cubic box with
> fixed no. of solvent molecules, what should i do.
> I have produce the pdb and library for solute and solvent both using
> xleap, now what should i do further for solvating my system with fix
> dimension box anf fixed no. of solvent molecule.

Amber doesn't provide such functionality. You might look at programs like
packmol to create an initial system.

Note that (in general) if you fix the number of solvent molecules, you won't
know the proper size of the box; or, if you fix the size of the box, you won't
know the proper number of solvent molecules.

The approach generally used inside tleap is to specify the "buffer" region,
which is the distance from the edge of the solute molecule to the edge of the
box. Then equilibration (including with constant pressure turned on) will
provide a useful description of the solvent environment. (You can do a sort
of trial&error with the buffer size to get the number of solvent molecules you
want, but this won't yield a box size given in advance.)

....hope this helps....dac

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Received on Sun Oct 19 2014 - 11:00:01 PDT
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