This particular tutorial is very useful in performing such analysis. Please go through it. http://www.mdtutorials.com/gmx/lysozyme/index.html

Hi,

Can you clarify your question well? Do you want to simulate the whole complex of both proteins or Do you want to simulate each protein separately?

Hi Neeraj Kumar,

I want to stimulate whole complex which I have got from docking software after docking.

Devender Arora Thankyou

Hi Parul Bhatt

If you are going to simulate the whole complex, just retrieve the complex as it is as it was the output of the docking tool, and follow the simple steps of simulation as per the link given by Devender Arora. Before simulation try to explore the interactions and interacting surfaces between both the proteins. If you still have issues, kindly ask them.

Cheers..!!

Good Day Parul Bhatt

I used HDock to perform my protein-DNA docking interaction and analyzed the output using PyMol and DSV. In DSV, I can identify the type of interaction in the complex using Receptor-ligand Interaction toolset.

However, I'm having difficulties in processing the HDock output for MD simulation as the PDB file of the complex is only contain list of ATOM (no HETATM). Do u have the same problem? Kindly assist me how to separate protein and DNA PDB file. Thank you in advance

https://docs.google.com/forms/d/e/1FAIpQLSfNpiah9wUc--jA7V1_42J2M3Cjlgtvgj-vDEasBIPXbEs9MQ/viewform?usp=pp_url

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