Re: [AMBER] Generating a solvent Box from organic solvent

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Mon, 12 Nov 2012 17:55:46 -0800

You could try building your own box by making a copy of your
acetic acid molecule, solvating it with the original residue,
then equilibrating the box before using it to solvate other molecules.


> x = copy ACX
> solvatebox x ACX 20 # larger than your expected box
> saveamberparm ...

 ...equilibrate...convert to pdb...

> ACXBOX = loadpdb ...
> solvatebox mymol ACXBOX 10


Mark Zottola <> wrote:

> I am trying to build a solvent box of acetic acid. I am going through the
> tutorial on making a non-standard residue to make an AMBER-friendly model
> of acetic acid. So far so good. But I have not seen anything in the mail
> reflector archive concerning the construction of a solvent box with
> anything but water. For the purposes of my project, adding some organic
> molecules to a water box (as is in a tutorial) will not be sufficient.
> Is there a published report concerning this process in the literature (a
> google search did not provide any leads), or is there a tutorial I missed?
> Any pointers to literature or other accessible instructions would be
> greatly appreciated.
> Thanks.
> Mark
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Received on Mon Nov 12 2012 - 18:00:02 PST
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