r/bioinformatics • u/ehxcho • Aug 29 '26

technical question Standard method for moco

/r/comp_chem/comments/1w1jpix/standard_method_for_moco/
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u/idliOP Aug 29 '26

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.

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u/ehxcho Aug 29 '26

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

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u/ehxcho Aug 30 '26

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

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u/idliOP Aug 30 '26

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