[gmx-users] unknown bond atom_type +

[Mark Abraham]

Hi,

Please keep discussion on the list.

I can only suggest you going looking for the + symbol in your grompp
inputs, because you've only shared a tiny fraction of your information...
like the whole grompp output (or at least error message without copy-paste
typos), and your GROMACS version. Probably you've mistakenly used some part
of the .rtp format in one of your .itp files.

Mark

On Wed, Aug 24, 2016 at 12:10 AM SAKO MIRZAIE <sako.biochem at gmail.com>
wrote:

> Dear Mark,
>
> what do you think about my problem?
>
> best regards,
>
> On 8/24/16, SAKO MIRZAIE <sako.biochem at gmail.com> wrote:
> > Hi,
> > it doesn't suggest me to look at the certain line or file.
> >
> > just before fatal error, and after the version of the software, it shows:
> > source code file: toppush.c, line: 270, if you mean that.
> >
> > On 8/24/16, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> >> Hi,
> >>
> >> The full version, I should say.
> >>
> >> Mark
> >>
> >> On Tue, 23 Aug 2016 23:54 Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >>
> >>> Hi,
> >>>
> >>> Does the future version of the error message suggest a line number for
> >>> you
> >>> to look at?
> >>>
> >>> Mark
> >>>
> >>> On Tue, 23 Aug 2016 23:11 SAKO MIRZAIE <sako.biochem at gmail.com> wrote:
> >>>
> >>>> Dear All,
> >>>>
> >>>> I am trying to do vacuum md on a huge polymer, f-127. I had to add sex
> >>>> residues to rtp file, but with know atom types. now, when I run the
> >>>> grompp, I got the following error:
> >>>>
> >>>> "unknown bond atom_type +"
> >>>>
> >>>> I checked my topology file and I have no any atom named "+". I don't
> >>>> know what does it mean. any help is appreciated.
> >>>>
> >>>> best regards
> >>>>
> >>>> --
> >>>> ***********************************************
> >>>> Sako Mirzaie
> >>>> PhD in biochemistry, Assistant Professor, science faculty,  Azad
> >>>> university of
> >>>> Sanandaj, Sanandaj, Iran
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
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> >>>>
> >>>
> >>
> >
> >
> > --
> > ***********************************************
> > Sako Mirzaie
> > PhD in biochemistry, Assistant Professor, science faculty, Islamic
> > Azad university of
> > Sanandaj, Sanandaj, Iran
> >
> > http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie
> >
> > http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie
> >
> > http://scholar.google.com/citations?user=viwZvVAAAAAJ&hl=en
> >
> > http://www.scopus.com/authid/detail.url?authorId=54886431500
> >
> > http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
> > https://www.researchgate.net/profile/Sako_Mirzaie/publications/
> >
>
>
> --
> ***********************************************
> Sako Mirzaie
> PhD in biochemistry, Assistant Professor, science faculty, Islamic
> Azad university of
> Sanandaj, Sanandaj, Iran
>
> http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie
>
> http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie
>
> http://scholar.google.com/citations?user=viwZvVAAAAAJ&hl=en
>
> http://www.scopus.com/authid/detail.url?authorId=54886431500
>
> http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
> https://www.researchgate.net/profile/Sako_Mirzaie/publications/
>