Hi Junmei,
thanks a lot for your great support.
Johannes
Am 2017-08-30 17:27, schrieb Junmei Wang:
> I see. Please add the torsional angle parameter of cc-cd-c3-c3 to
> gaff2.dat
> "cc-cd-c3-c3 1 0.157 180.0 3"
>
> I will check gaff2.dat and make sure all the equivalent parameters
> exist.
>
> Thanks a lot.
>
> Junmei
>
> On Wed, Aug 30, 2017 at 5:28 AM, Traeg, Johannes
> <johannes.traeg.fau.de>
> wrote:
>
>> 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 Thu Aug 31 2017 - 01:30:02 PDT
