I have been working on the design of covalent inhibitors, which are covalently bound to the cysteine side chain. it would be really helpful if somebody would guide how to modify the processed protein file after initial simulation step in gromacs.
Hi Tenuj,
There is a page on gmx web that deals with this:
https://manual.gromacs.org/current/how-to/topology.html
Since, it is covalently bonded, you need to create a new Cysteine residue (e.g. CYQ), and take backbone parameters from the forcefield that you are going to use. For the rest, you need to create/parameterized bonds, angle, partial charges, etc, for that there are multiple programs are there (it can be done in AmberTools/ ACPYPE [Article ACPYPE-Antechamber python parser interface
], etc).Once, it is done, I prefer to run a short simulation for the modified residue only to check whether it is stable or not. If stable, you can introduce it in the ff and simply run it.
Creating parameters is tricky, you need to be careful. Also, please backup your ff first if you are going to edit any file.
Good luck.
Dear Tanuj Sharma ,
I hope that the following research article would help you in great:
Article Molecular docking and dynamics simulation revealed the poten...
I agree with the above-posted answer. Follow any tutorials and start; if you face any problem at that time, then post a new trial.
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