Hi,
You could use Packmol to construct a monolayer wit a PDB file, please see the example in the program website. The second and third example can be useful
http://www.ime.unicamp.br/~martinez/packmol/examples.shtml
Good luck
--------------------------------------------------------------------
Stéphane Abel, Ph.D.
CEA Saclay DSV/ISVFJ/SB2SM
Institut de Biologie Intégrative de la Cellule (I2BC)
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
________________________________________
De : Elvis Martis [elvis.martis.bcp.edu.in]
Envoyé : vendredi 28 juillet 2017 18:35
À : AMBER Mailing List
Objet : Re: [AMBER] How to make a phenol monolayer
Hi,
Since I am not aware of any method of building monolayers in AMBER, I suggested an alternative method.
Any non-protein, non-RNA, non_DNA molecules need to supply with additional force field parameters, not present gaff or gaff2 force fields, to be able to save the topology and coordinate file.
I am not saying that you cannot build monolayer using AMBER, only that I am not aware of how it is done. Some developer will give you the method to do it with AMBER.
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: Ramin Salimi <ramin.salimi01.utrgv.edu>
Sent: 28 July 2017 21:31
To: AMBER Mailing List
Subject: Re: [AMBER] How to make a phenol monolayer
Hi
I'm askong this question for I haven't worked with Maestro-GUI: Why do we need to worry about having necessary parameters while using it?
Also, you're saying that we cannot build a monolayer with Amber?
Ramin
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________________________________
From: Elvis Martis <elvis.martis.bcp.edu.in>
Sent: Friday, July 28, 2017 8:52:31 AM
To: AMBER Mailing List
Subject: Re: [AMBER] How to make a phenol monolayer
Hi,
No No I haven't commented on force fields. if its phenol then gaff or gaff2 should be able to deal with them.
I have only given you an alternative method how to build a monolayer using maestro-GUI.
Once you have built the desired monolayer, you can export it as pdb and load it in leap to save the prmtop and inpcrd files provided you have necessary parameters for phenol.
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: Ramin Salimi <ramin.salimi01.utrgv.edu>
Sent: 28 July 2017 21:18
To: AMBER Mailing List
Subject: Re: [AMBER] How to make a phenol monolayer
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 Sat Jul 29 2017 - 06:00:03 PDT
