First i suggest reading
https://ambermd.org/AmberModels.php
Especially the mix and match caution.
Then, if it's a combination that had been tested together but still doesn't
work for you, reply back with those details.
On Mon, Mar 4, 2024, 8:31 PM Sasha Buzko via AMBER <amber.ambermd.org>
wrote:
> 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 - 18:00:03 PST
