What force field should I use for a protein co-complex incorporating nucleotides?

13 March 2022 1 8K Report

I have a system of a protein co-complex which behaves like a polymerase. One of them recognises the binding site and other catalyses the reaction.

I am confused between ff14SB and PARMbsc1. What should I use ?

Aashish Bhatt

Dear Hindol,

For force field parameters you can use ff14SB for protein and PARMbsc1 force field is for Nucleotides(DNA and RNA).

It would help if you incorporated both the force field parameter.

Using the PARMbsc1 force field shows good agreement for the experimental results.

Please look amber-20 force field manual and especially "Molecular mechanics force fields".

Also, look at "https://www.youtube.com/watch?v=iQThYDiJs7c&ab_channel=CHARMM-GUI" choosing the force field paramter.

Hopefully, it will help.

Best Regards

Aashish

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