From: Piotr Fajer <pfajer.fsu.edu>
Date: Wed, 18 Jul 2018 15:53:39 +0000
Many thanks. Unfortunately, I am now getting an error message that CUDA does not support 12-6-4 LJ potential. I am using Amber16, does Amber18 support it ?
Peter
> On Jul 18, 2018, at 7:16 AM, David A Case <david.case.rutgers.edu> wrote:
>
> [From Kennie Merz]:
>
> There are 12-6 and 12-6-4 Ca(II) nonbonded parameters available, but they were designed to reproduce aqueous phase properties. How they will work with Ca(II) binding to an EF-hand is anyone's guess. This paper from the York lab highlights some of the challenges you might face: York & co-workers JPCB 2015, 119, 15460. Other than that MCPB.py is another way to go to build a bonded model. You have a super interesting problem, but some tuning will be in order if you want to go the nonbonded model route is my guess. Good luck!
>
> Kennie
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=HPMtquzZjKY31rtkyGRFnQ&r=8waEScVAJus7pLy7oGBweQ&m=scFlnxQR8Zg7OkJ9DELmu0jSyhaJQpThHDKYGxjE820&s=VxEUuItJYxoLLxUUg7Ki56LS_ZHSCAg4SH5HO9VmIx4&e=
