Re: [AMBER] How to create the .off/.lib file of the equilibrated non-aqueous solvent box?

From: David A Case <>
Date: Sun, 27 Nov 2016 16:16:12 -0500

On Sun, Nov 27, 2016, Yew Mun Yip wrote:
> I have generated and equilibrated an ethanol solvent box using AMBER. I
> wish to ask how do I create the .off/.liv file of my non-aqueous solvent
> box so that I can use to solvate my solute?

tleap can load a pdb file with the coordinates, that the SaveOff command
will create the library file. Be sure to use the "set <unit> box" command
to set up the box size before issuing the SaveOff command. e.g.:

    <load needed amber libraries and parm files here>
    x = loadpdb <your-pdb-file>
    set x box { <a> <b> <c> } where a,b,c are the box dimesions
    saveOff x ethanolbox.lib

...good luck...dac

AMBER mailing list
Received on Sun Nov 27 2016 - 13:30:04 PST
Custom Search