[AMBER] Using a box of organic solvent

From: Alessandro LANDI <alelandi1.unisa.it>
Date: Fri, 31 May 2019 12:42:08 +0200

Dear all,

I have read the message "Re: [AMBER] Organic solvent box - Amber do not see
the molecule but its atoms" (appended at the end of this e-mail), and I
have a closely related question.

Starting from a pdb file retrieved from the "ATB" repository (link:
https://atb.uq.edu.au/) and using the Packmol software, I have been able to
build a cubic box of 500 THF molecules. I have also evaluated the RESP
charges and all the parameters needed in AMBER for that solvent, by using

My question is: in order to use THF as an explicit solvent in AMBER
simulations, which files do I have to use and in which folder do I need to
put them?
Finally, which commands do I need to use in Leap, (maybe via "solvateoct"?)
to use this THF box I have built?

As a newbie, any help will be appreciated.
Thanks in advance.

From: David A Case <david.case.rutgers.edu>
Date: Tue, 24 May 2016 09:03:37 -0400

On Tue, May 24, 2016, Stregone wrote:
*> *
*> I am doing a acetone box. I did find useful information in *
*> - http://archive.ambermd.org/201211/0214.html
<http://archive.ambermd.org/201211/0214.html> *
*> - http://archive.ambermd.org/200908/0377.html
<http://archive.ambermd.org/200908/0377.html> *

Once you create an acetone UNIT (molecule), you can either use packmol
to create a box full of these (just save in pdb format), or you can
use solvateBox to build this.

*> I realised that Amber only see the atoms, but not the molecule. *

How did you arrive at this conclusion? To be of any help, we need to know
exactly what commands you used, and what you saw. How did you create the
acetone unit?

*> I have been using the pdb and mol2 files from the the project in
R.E.DD.B. *

This is probably fine: we just don't know (from your description) what you
in LEaP.


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Received on Fri May 31 2019 - 04:00:02 PDT
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