Re: [AMBER] OE tools help

From: Raman Preet Singh <>
Date: Thu, 10 Sep 2020 09:58:58 +0000

Hi Debarati,

I generated conformors using below command
prompt> omega2 drugs.smi drugs.oeb.gz (instead of .smi, you can also use .sdf and .mol2 files – see the OMEGA manual for details). The oeb.gz file was then used in ROCS.

Regarding using MD equilibrated structures, I use CHARMM FF which generates a pdb and a psf file (CHARMM FF because CHARMM-GUI makes life easier for me as I work on nanoparticles, small molecules and carbohydrates which can be easily generated and parameterized in CHARMM-GUI).

After equilibrating the protein (obtained from PDB or homology models) in TIP3 water for 5-10 ns (you may have to optimize time for your protein), I load the trajectory in VMD and save the last frame as pdb. The CHARMM formatted pdb generated by VMD does not have CONECT records (those are in the psf file) so you can combine pdb and psf (the same psf that is used for equilibration) using psf2pdb. The generated pdb is now ready for use in FRED (or any other docking software)!

Hope that helps!


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 - 03:00:03 PDT
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