I am working with a protein that has two sodium and ions which are important for the binding of the ligand and overall action of the protein. I have prepared the receptor file using AutoDockTools and the assigned Gasteiger charges by ADT to the sodium ions were 0.08 and 0.074. So, my question is should I proceed with the charges assigned by ADT or should I manually edit the pdbqt file and assign a +1 charge to the sodium ions. I will be docking with VINA. Also, how much will the presence of the charges affect the binding of the ligand?
Hi Archishman,
AutoDock Vina ignores all atomic charges, so you need to use AutoDock 4.
AutoDock 4 is fine. You can also try to prep with UCSF Chimera...maybe that could help.
cheers!!
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Dear colleagues,
Department of Pharmacy, Universitas Muhammadiyah Palangkaraya openly inviting researchers with expertise in the field of Molecular Docking to join the new journal that will be released in early 2021, both as an editorial board and as peer-reviewers.
We will call this journal "Journal of Molecular Docking" or "J. Mol. Docking", with a very specific aim and scope, namely various research in the field of science and health using Molecular Docking as its main method.
Currently we are still preparing the journaling platform with OJS 3.1.1.2 and will start collecting articles as soon as the editorial board and peer-reviewer members are gathered. The link for this new journal is http://journal.umpalangkaraya.ac.id/index.php/jmd.
It should be noted that this position is voluntary, so all editors and reviewers will not receive any rewards in the form of funds. However, we will provide a certificate of appreciation for each manuscript handled, both as an editor and reviewer.
The target of this new journal is to be indexable by DOAJ after the first year and indexed by Scopus and/or ESCI WoS after the fifth year.
For this reason, we expect the willingness and participation of Molecular Docking researchers to be directly involved in the development of this new journal so that later it can become a publication benchmark for research with the molecular docking method.
Once again, we are grateful for the participation of all researchers and hope for their support to be able to create and grow this new journal.
Best regards,
Mohammad Rizki Fadhil Pratama
Assistant Professor of Medicinal Chemistry
Universitas Muhammadiyah Palangkaraya
http://orcid.org/0000-0002-0727-4392
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