Hi every body. I want to do a MD in gromacs for protein but it have a non standard residue. Somone who tell me how I can to do it? Which programs I should to usage? or some tutorial that I can to do or see for this. The protein is GABA AMINOTRANSFERASE but this contain whit PLP covalent bond to LYS residue. THANKS
Hi Jose,
You can try AMBERTOOLS to generate FF parameters for a protein which has unknown residues.
Please go through the this tutorial:
https://ambermd.org/tutorials/basic/tutorial4b/index.php
You need to create force field parameter for PLP with covalent bounded Lysine residue.
You can use Antechmber for designing a force field parameter.
http://ambermd.org/tutorials/basic/tutorial5/
You can check my paper supporting information.
https://www.tandfonline.com/doi/abs/10.1080/07391102.2021.1975564?journalCode=tbsd20
Use the solution builder module of CHARMM-GUI to auto-prepare force field parameters of protein and non-standard residue, within water solution.
The output files will be ready to proceed with minimization.
Minimize the file and check for the components of .gro file properly.
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