Re: [AMBER] OE tools help

From: Raman Preet Singh <>
Date: Thu, 10 Sep 2020 09:36:25 +0000

Hi Debarati,

OMEGA prompt was omega2 drugs.smi drugs.oeb.gz

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From: Debarati DasGupta<>
Sent: 09 September 2020 18:11
To: Raman Preet Singh <><>;<>
Subject: OE tools help

Hello Raman,
Thanks for the reply.
Actually I am trying to do some docking with FRED, but before that they need 2 steps : Preparing the ligand and preparing the receptor for docking.
There are 2 tools Spruce4docking and Make_receptor tool but they are not able to take a MD equilibrated structure as input for a receptor.
I just needed some info how to feed in an equilibrated MD structure as a receptor to FRED. Also I m trying to generate conformers in OMEGA for my PPI dataset. I see that they have a tool “Filter” which they say should be used prior to OMEGA... Have you used omega or oeomega as I see both these exe files in bin and cannot understand the difference between the two. Could you share how you did use OMEGA for conformer generation?

Sent: Wednesday, September 9, 2020 5:48:36 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] OE Tool kit

I have briefly used OMEGA and ROCS from OE. For docking, I use Vina. BTW, what is your specific question (parametrizing a docked ligand, etc….)?


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Received on Thu Sep 10 2020 - 03:00:02 PDT
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