Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer

From: Renato Araujo <renatoacufpa.gmail.com>
Date: Sun, 17 May 2020 11:31:37 -0300

right

have use pymol just to save to PDB and see if you still get the same error.

Att.,

Renato Costa

Em domingo, 17 de maio de 2020, Lod King <lodking407.gmail.com> escreveu:

> 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 - 08:00:02 PDT
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