Dear all,
Le 30/03/2026 à 20:01, ElBagoury, Abdulrahman Walid Attia Ibrahim via
AMBER a écrit :
> Thank you for clarifying this and I will try it as well. I also appreciate both the video and your article with the quick tips.
I hope it is helpful to many, even if the AMBER manual contains a lot of
important and interesting recommandations,
reading the chapters is a very good starting point.
>
>
> Finally, regarding the usage of the Modeller part, should I perform this step prior to the docking and MD simulation protocols that I previously provided?
I'm a bit conservative on this part, and I prefer to have all systems
exactly the same, so I would complete the PDB first,
and dock ligands afterwards, even if it may have little influcence.
Electrostatics for instance may have inconsistencies
if some side chains are incomplete and/or truncated. Everything depends
on the distance of the missing residues
from the binding site.
>
>
> Also, concerning my previous protocol, are the steps in the correct order, and would it be appropriate to proceed with this workflow, or would you recommend any modifications?
For the same reasons as above, I prefer to NOT switch between many
residues, and to be consistent
between force fields and software. I would better use Chimera for
protein and ligand preparation,
then DOCK6 then AMBER for MD simulations. To set up your system, you can
even use the excellent
AMBERMDPrep protocole from Daniel ROE, where all steps are verified and
validated :
https://pubs.aip.org/aip/jcp/article-abstract/153/5/054123/1065686/A-protocol-for-preparing-explicitly-solvated
Concerning the reasons for the failures, often I see two major causes:
1) hydrogen names are not the same between software (as already indicated)
2) ligand charge is not correct
HTH,
Stéphane
--
Associate Professor, USBB, UMR 6286 CNRS, Bioinformatique Structurale
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 8, 44322 Nantes cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.us2b.univ-nantes.fr/ -http://www.steletch.org
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Received on Wed Apr 01 2026 - 03:00:02 PDT
