Re: [AMBER] Calcium force fields

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
>
>
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Received on Wed Jul 18 2018 - 09:00:03 PDT
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