Hello Junmei,
i also tried with 5-ethyl-1H-1,2,3-triazole and got the correct dihedral
parameters. However, for 4-ethyl-1H-1,2,3-triazole it does not work.
The difference between both molecules is that in one case antechamber
ascribes the dihedral c3-c3-cc-cd (5-ethyl) and in the other case
antechamber ascribes the dihedral c3-c3-cd-cc (4-ethyl). The latter
dihedral defaults to the dihedral X-c3-cd-X, while the first one does
not default to X-c3-cc-X, but takes the value of the explicit dihedral
c3-c3-cc-cd. However, due to the equivalence of cd and cc, one would
expect to get the same values for both dihedrals.
How would you proceed to solve this problem?
Best regards
Johannes
Am 2017-08-29 16:02, schrieb Junmei Wang:
> Also, cd-cc-c3-c3 was introduced only in gaff2 (0.157, 0.0, 3). In
> gaff,
> the force constant of cd-cc-c3-c3 is 0.0 (X-cc-c3-X 6 0.0 3.0).
>
> Best
>
> Junmei
>
> On Tue, Aug 29, 2017 at 9:54 AM, Junmei Wang <junmwang.gmail.com>
> wrote:
>
>> Hello, Johannes,
>>
>> When you ran parmchk2, did you specify to use gaff2 with "-s 2"? The
>> default FF to use is gaff, not gaff2.
>>
>> I constructed two triazole molecules (ethyl triazole and
>> 5-ethyl-1H-1,2,3-triazole) and assigned both gaff and gaff2 atom
>> types. I
>> didn't find a problem with the four frcmod files produced by parmchk2.
>>
>> Please also use "-at gaff2" when you run antechamber to assign gaff2
>> atom
>> types.
>>
>> Please let me know if you have more questions.
>>
>> Best
>>
>> Junmei
>>
>> On Tue, Aug 22, 2017 at 4:47 AM, Traeg, Johannes
>> <johannes.traeg.fau.de>
>> wrote:
>>
>>> Hi AMBER users,
>>>
>>> I'm having trouble with a GAFF2 force field that I generated with
>>> ANTECHAMBER/LEAP. My molecule contains a triazole unit with an ethyl
>>> group connected to one of the carbon atoms of triazole. ANTECHAMBER
>>> correctly recognizes the atom types and, hence, my molecule contains
>>> the
>>> dihedral CC-CD-C3-C3 (CC and CD are identical in GAFF/GAFF2). The
>>> .prmtop file lists the following parameters for this dihedral:
>>>
>>> force constant = 0.0
>>> phase = 0.0
>>> periodicity = 3
>>>
>>> However, the GAFF2.dat file (Amber16) lists the following parameters
>>> for
>>> the dihedral CD-CC-C3-C3, which should be identical to CC-CD-C3-C3
>>> (due
>>> to the equivalence of CC and CD):
>>>
>>> force constant = 0.157
>>> phase = 180.0
>>> periodicity = 3
>>>
>>> Can anyone help me out with this problem?
>>>
>>> Thanks in advance and best regards,
>>>
>>> Johannes
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
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Received on Wed Aug 30 2017 - 02:30:04 PDT
