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
quit
...good luck...dac
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Received on Sun Nov 27 2016 - 13:30:04 PST
