r/bioinformatics • u/ehxcho • 3d ago

technical question Standard method for moco

/r/comp_chem/comments/1w1jpix/standard_method_for_moco/
1 Upvotes

100% Upvoted

4 comments sorted by

1

u/idliOP 3d ago

Use AutoDock4 (AD4) forcefield maps with Vina. You will need to manually add custom Mo parameters (radius and well-depth) into your parameter file, generate new grid maps using AutoGrid4, and then run Vina with those custom maps.

But I think if you have some time, consider looking at programs like GOLD & GLIDE, these handle metal transitions much better thwn Vina.

2

u/ehxcho 3d ago

thank you for that, btw are GOLD and GLIDE open source because I'm studying to dock this for my undergrad thesis and does the process of parametizing manageable for newbie like me

2

u/ehxcho 2d ago

thank youu so much for this I used autodock 4 and custom parametization and it work thank u so much

2

u/idliOP 2d ago

You're most welcome! Sorry I missed your earlier reply! Glad that it worked out for you!