Hi,
My molecule is intact, I don’t need more Hydrogen in my molecule, or it
will make my molecule differ from my original idea.
On Sun, May 17, 2020 at 6:13 AM Renato Araujo <renatoacufpa.gmail.com>
wrote:
> Hi
>
> Try to use pymol to add hydrogen and save the molecule in PDB.
>
> Then use the antechamber and see if it works
>
> Att.,
>
> Renato Costa
>
> Em sáb., 16 de mai. de 2020 às 23:00, Lod King <lodking407.gmail.com>
> escreveu:
>
> > Sorry that I did not attach the file, here it is the furazan molecule in
> > mol2.
> > .<TRIPOS>MOLECULE
> > *****
> > 9 9 0 0 0
> > SMALL
> > GASTEIGER
> >
> > .<TRIPOS>ATOM
> > 1 O 0.0008 -1.2130 -0.2258 O.3 1 UNL11
> > -0.1569
> > 2 N 1.1196 -0.3508 -0.2616 N.4 1 UNL11
> > -0.2470
> > 3 N -1.1188 -0.3520 -0.2618 N.4 1 UNL11
> > -0.2470
> > 4 C 0.6667 0.9398 -0.0901 C.2 1 UNL11
> > 0.0453
> > 5 C -0.6675 0.9391 -0.0898 C.2 1 UNL11
> > 0.0453
> > 6 H 1.8455 -0.6256 0.3944 H 1 UNL1
> > 0.1958
> > 7 H 1.3533 1.7562 0.0709 H 1 UNL1
> > 0.0843
> > 8 H -1.8454 -0.6281 0.3927 H 1 UNL1
> > 0.1958
> > 9 H -1.3550 1.7546 0.0717 H 1 UNL1
> > 0.0843
> > .<TRIPOS>BOND
> > 1 1 2 1
> > 2 1 3 1
> > 3 2 4 1
> > 4 3 5 1
> > 5 4 5 2
> > 6 2 6 1
> > 7 4 7 1
> > 8 3 8 1
> > 9 5 9 1
> >
> > On Sat, May 16, 2020 at 6:49 PM David A Case <david.case.rutgers.edu>
> > wrote:
> >
> > > On Sat, May 16, 2020, Lod King wrote:
> > > `
> > > >
> > > >Note that it worked when I use pdb format instead of mol2 format,
> > although
> > > >I often use mol2 file to generate my prepc and frcmod files.
> > >
> > > Glad it seems to be working. I understand that you may not be able to
> > > share your input files with others. But without a way to reproduce the
> > > problem, it is unlikely that anyone on the list will be able to provide
> > > real help.
> > >
> > > ....dac
> > >
> > >
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Received on Sun May 17 2020 - 07:00:02 PDT
