[AMBER] Suitable water model for solvent-exposed structures?

From: Sasha Buzko via AMBER <amber.ambermd.org>
Date: Tue, 5 Mar 2024 01:30:39 +0000

Dear All,
I'm running explicit solvent simulations of a globular protein with a long linker connected to a helical peptide. So far, I've tried OPC water model and I'm seeing instability of the helix and an overall drift of the connected structure to the carrier protein. It's basically trying to fold into the protein.
I'm wondering how much of it is real and how much is due to underestimated solvation.
I'm trying TIP4PEW as well and thinking about TIP5P. The latter looks good on paper but I've seen conflicting opinions about its performance. Besides, its setup seems to be less than trivial.

Does anyone have experience modeling these types of structures? What water model worked best for a highly solvent-exposed structure?

Thank you in advance!

Sasha

---
Oleksandr "Sasha" Buzko
Computational Biology
ImmunityBio
9922 Jefferson Blvd
Culver City, CA 90230
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Received on Mon Mar 04 2024 - 18:00:02 PST