Hi,
As far as I know there's no easy way to do this in LEaP. You may want
to try 'packmol' instead.
-Dan
On Wed, Nov 24, 2021 at 7:36 AM Damiano Spadoni
<Damiano.Spadoni.nottingham.ac.uk> wrote:
>
> Seems like I can't find any similar topic in the AMBER community, perhaps I should reformulate my question:
> Is it anyway possible to create an octahedral box of mixtures of solvents different from water in LEAP?
>
> Kind regards,
> Damiano
> ________________________________
> From: Damiano Spadoni <Damiano.Spadoni.nottingham.ac.uk>
> Sent: Tuesday, November 23, 2021 8:26 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] Protein in mixed of solvents
>
> Dear Amber community,
>
> I want to create on tLEAP a system that is composed of a protein in a mixture of solvents (DME and DOL 3:2) enclosed in an octahedral truncated box.
> I now Packmol is extensively used to solvate biomolecules in mixed solvents but it does not have the octahedral truncated box option: cubic or spheric only.
> I'd like to know of possible workaround(s) to generate similar systems.
> What if, in a second time, I want to add organic salts at specific concentration (molarity)?
>
> Best regards,
> Damiano
>
>
>
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Received on Wed Dec 01 2021 - 06:00:03 PST
