[gmx-users] unknown bond atom_type +

[Mark Abraham]

Hi,

You should really not be starting new work with ancient no-longer-supported
code versions... Running grompp on the server is typically not a great
idea. What is the full output that grompp writes to the terminal? Hint, it
is unlikely to be called em_out.log, which might be a file you wrote with
mdrun?

Mark

On Wed, Aug 24, 2016 at 12:59 AM SAKO MIRZAIE <sako.biochem at gmail.com>
wrote:

> I am using gromacs 4.5. my grompp input files are just topology and a
> gro file. neither of them have "+". when I add the "+" to the
> ffnonbonded file with wrong parameters, it error is disappeared. I am
> really confused. I am using a server for my simulations and the
> em_out.log lacks the error.
>
>
>
> On 8/24/16, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> > 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
> >> >>>>
> >> >>>> * Please search the archive at
> >> >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> >>>> posting!
> >> >>>>
> >> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >>>>
> >> >>>> * For (un)subscribe requests visit
> >> >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >> >>>> or
> >> >>>> send a mail to gmx-users-request at gromacs.org.
> >> >>>>
> >> >>>
> >> >>
> >> >
> >> >
> >> > --
> >> > ***********************************************
> >> > 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/
> >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a
> > mail to gmx-users-request at gromacs.org.
> >
>
>
> --
> ***********************************************
> 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/
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>