Dear Fabian,
The protocol you mentioned earlier is perfectly fine. Just out of
curiosity, you can even also pregenerate the charges using antechamber and
then redock on original pdb complex to achieve near native conformation and
then follow the protocol you mentioned earlier.
Regards,
Dhaval
On Tuesday, December 11, 2018, Fabian Glaser <fabian.glaser.gmail.com>
wrote:
> 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,
>
> Best,
>
> Fabian
>
> 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
> Web http://bku.technion.ac.il/
> Tel +972 (0) 4 8293701
>
> > On 9 Dec 2018, at 23:08, David Case <david.case.rutgers.edu> 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 http://upjv.q4md-forcefieldtools.org/RED/) 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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--
Sincerely yours,
Dhaval Patel | PhD
The M. S. University of Baroda, Vadodara.
Lab: Biophysics & Structural Biology,
Indian Institute of Advanced Research,
Gujarat, INDIA. +91 9925450504
pateldhaval.in.gmail.com; dhaval.iiar.res.in
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Received on Fri Dec 21 2018 - 21:30:03 PST
