Hello,
Yeah, pmemd.cuda of Amber 18 supports LJ 12-6-4 potential.
Best,
Qinghua
On 07/18/2018 05:53 PM, Piotr Fajer wrote:
> 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 - 10:00:02 PDT
