Dear Mattei,
> 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?
You simply need to use your newly designed EtOH box as you would use
the TIP3P one in LEaP. See the "solvatebox" or "solvateoct" commands
in LEaP in the AmberTools manual.
- you load the FF of your choice using a leaprc...cmd file in LEaP
- you load the FF library of your EtOH box
- you load the FF library of your molecule
- you solvate your molecule using your EtOH box
regards, Francois
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Received on Sat Feb 05 2011 - 01:30:02 PST
