Re: [AMBER] ligand charges for md

From: Fabian Glaser <>
Date: Tue, 11 Dec 2018 18:33:08 +0200

This is great, thanks a lot!

I checked and antechamber works fine for this ligand, great! Then I have a follow up question:

In this case, I need to dock this ligand into its receptor, and then MD with some of the best docking results, since I don’t have the ligand - protein complex. As I understand the antechamber energy and charges will be dependent on the specific geometry of the ligand, so I guess those are the steps to follow:

1) dock the ligand using my initial charges (calculated from an initial guess, in this guess a PDB geometry)
2) choose my best conformations from docking
3) recalculate antechamber for each ligand docking results I intend to run MD
4) create prmtop and run MD with each new antechamber result for the complex

Is this a generally correct protocol?
And then

Thanks a lot, hope this are not too trivial questions for you,



Fabian Glaser PhD

Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Tel +972 (0) 4 8293701

> On 9 Dec 2018, at 23:08, David Case <> wrote:
> On Sun, Dec 09, 2018, Fabian Glaser wrote:
>> I would like to ask what would be a reasonably correct way to assign
>> charges for the following ligand:
> The simplest way is to get am1-bcc charges via antechamber (using the
> "-c bcc" flag). Generally speaking, tests of this charge model over
> many ligands shows good performance, but that doesn't mean it is by any
> means the best choice for every ligand.
> A second, popular, approach is to get RESP charges. The R.E.D. web
> service (at is very popular
> for working a single ligand. And their database may already have
> charges for your ligand--it's worth a check.
> I'm sure that in principle, one can use antechamber for this purpose,
> even with Gaussian. But someone else will have to supply details here.
> ...hope this helps....dac
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Received on Tue Dec 11 2018 - 09:00:03 PST
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