Re: [AMBER] Protein in mixed of solvents

From: Damiano Spadoni <Damiano.Spadoni.nottingham.ac.uk>
Date: Wed, 24 Nov 2021 12:36:07 +0000

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 Nov 24 2021 - 05:00:02 PST
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