Re: [AMBER] How to make a phenol monolayer

From: Ramin Salimi <ramin.salimi01.utrgv.edu>
Date: Fri, 28 Jul 2017 15:48:30 +0000

Hi Elvis
Thanks so much for the reply
Do you are saying there isn't any forcefield to employ in Amber?
My other question is given a forcefield, how can one build a monolayer of a phenol, for instance?

Regards
Ramin

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________________________________
From: Elvis Martis <elvis.martis.bcp.edu.in>
Sent: Thursday, July 27, 2017 8:48:29 PM
To: AMBER Mailing List
Subject: Re: [AMBER] How to make a phenol monolayer

Hi,
I am not sure how to do it AMBER but there is a way you can do it using Maestro-GUI (free to download).
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.schrodinger.com%2Fkb%2F1006&data=02%7C01%7Cramin.salimi01%40utrgv.edu%7Cba6c5400ae22442be72f08d4d56b9d87%7C990436a687df491c91249afa91f88827%7C0%7C0%7C636368105583151365&sdata=fAreC9SztjfTZnK9jeX0nYxL0NJ2w1dEHr0%2BDEuQicw%3D&reserved=0 here is the link.
This tutorial is to make membranes but you can tweak this to make phenol monolayer as well.

Best Regards
Elvis Martis
Mumbai, INDIA.

________________________________________
From: Ramin Salimi <ramin.salimi01.utrgv.edu>
Sent: 28 July 2017 03:06
To: amber.ambermd.org
Subject: [AMBER] How to make a phenol monolayer

Dear All

I have been trying to construct a phenol monolayer, but I don't know how to make one layer of that for my simulation.I mean, given the phenol pdb file, how can we build a layer out of that?


Any help would be greatly appreciated

Kind Regards

Ramin

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Received on Fri Jul 28 2017 - 09:00:02 PDT