Re: [AMBER] Gromber failed.

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 3 Nov 2016 06:18:04 -0400

Those force fields use a different functional form for the dihedrals (Ryckaerts-Bellemans) I believe, which is equivalent to what amber uses as long as the phase shifts are either 0 or 180 degrees.

However, ParmEd does not yet have the ability to convert between the two functional forms. So even though it should be possible, I don't think it is yet.

HTH,
Jason

--
Jason M. Swails 
> On Nov 2, 2016, at 10:05 PM, Dd H <ddhecnu.gmail.com> wrote:
> 
> You mean I should upgrade to the newest version?
> 
>> On 3 November 2016 at 09:58, Nhai <nhai.qn.gmail.com> wrote:
>> 
>> The newest version in AT16 is 2.6.1
>> 
>> Hai
>> 
>>> On Nov 2, 2016, at 9:13 PM, Dd H <ddhecnu.gmail.com> wrote:
>>> 
>>> I checked the version of parmed using this command: "parmed -v" and it's
>>> version 2.0.5
>>> 
>>> 
>>>>> On 3 November 2016 at 09:00, Hai Nguyen <nhai.qn.gmail.com> wrote:
>>>>> 
>>>>> On Wed, Nov 2, 2016 at 8:56 PM, Dd H <ddhecnu.gmail.com> wrote:
>>>>> 
>>>>> Hi Jason,
>>>>> The system contains a protein, a ligand, water and counter ions, and
>>>>> AMBER99SB force field and GAFF are used. I think the input files are
>>>>> ordinary. So I don't know why it failed.
>>>>> 
>>>> 
>>>> which version you're using? you might want to upgrade to AmberTools16
>>>> 
>>>> Hai
>>>> 
>>>> 
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Received on Thu Nov 03 2016 - 03:30:03 PDT