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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> > AMBER.ambermd.org
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>
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Received on Wed Aug 30 2017 - 08:30:02 PDT
