[gmx-users] unknown bond atom_type +
Mark Abraham
mark.j.abraham at gmail.com
Wed Aug 24 01:34:27 CEST 2016
Hi,
You can upload files to any file-sharing service and share links, but the
list doesn't accept attachments to send to thousands of people.
More importantly, your .rtp files are inputs for pdb2gmx, not grompp, so
something about your reporting doesn't make sense. But we still can't see
your error messages, so I guess I'll have to give up trying to help.
Mark
On Wed, Aug 24, 2016 at 1:27 AM SAKO MIRZAIE <sako.biochem at gmail.com> wrote:
> May I upload my input and output files? solving this problem is really
> critical for me.
>
> thanks,
>
> On 8/24/16, SAKO MIRZAIE <sako.biochem at gmail.com> wrote:
> > I have added the following residue to rtp:
> > [ PES ]
> > [ atoms ]
> > H1 HO 0.405002 1
> > O1 OH -0.603301 2
> > C1 CT 0.127400 3
> > C2 CT 0.130400 4
> > H2 H1 0.035700 5
> > H3 H1 0.035700 6
> > H4 HC 0.042700 7
> > H5 HC 0.042700 8
> >
> > [ bonds ]
> > H1 O1
> > O1 C1
> > C1 C2
> > C1 H2
> > C1 H3
> > C2 H4
> > C2 H5
> > C2 +O1
> >
> > [ PEO ]
> > [ atoms ]
> > O1 OH -0.431600 1
> > C1 CT 0.130400 2
> > C2 CT 0.130400 3
> > H1 H1 0.042200 4
> > H2 H1 0.042200 5
> > H3 HC 0.043200 6
> > H4 HC 0.043200 7
> >
> > [ bonds ]
> > O1 C1
> > C1 C2
> > C1 H1
> > C1 H2
> > C2 H3
> > C2 H4
> > -C2 O1
> > C2 +O1
> >
> > [ PTF ]
> > [ atoms ]
> > O1 OH -0.437601 1
> > C1 CT 0.140100 2
> > C2 CT -0.120100 3
> > C3 CT 0.127400 4
> > H1 H1 0.065700 5
> > H2 HC 0.045367 6
> > H3 HC 0.045367 7
> > H4 HC 0.045367 8
> > H5 HC 0.044200 9
> > H6 HC 0.044200 10
> >
> > [ bonds ]
> > O1 C1
> > C1 C2
> > C1 C3
> > C1 H1
> > C2 H2
> > C2 H3
> > C2 H4
> > C3 H5
> > C3 H6
> > -C2 O1
> > C3 +O1
> >
> >
> >
> > [ PPO ]
> > [ atoms ]
> > O1 OH -0.437601 1
> > C1 CT 0.140100 2
> > C2 CT -0.120100 3
> > C3 CT 0.127400 4
> > H1 H1 0.065700 5
> > H2 HC 0.045367 6
> > H3 HC 0.045367 7
> > H4 HC 0.045367 8
> > H5 HC 0.044200 9
> > H6 HC 0.044200 10
> >
> > [ bonds ]
> > O1 C1
> > C1 C2
> > C1 C3
> > C1 H1
> > C2 H2
> > C2 H3
> > C2 H4
> > C3 H5
> > C3 H6
> > -C3 O1
> > C3 +O1
> >
> > [ PTE ]
> > [ atoms ]
> > O1 OH -0.431600 1
> > C1 CT 0.130400 2
> > C2 CT 0.130400 3
> > H1 H1 0.042200 4
> > H2 H1 0.042200 5
> > H3 HC 0.043200 6
> > H4 HC 0.043200 7
> >
> > [ bonds ]
> > O1 C1
> > C1 C2
> > C1 H1
> > C1 H2
> > C2 H3
> > C2 H4
> > -C3 O1
> > C2 +O1
> >
> >
> >
> > [ PEE ]
> > [ atoms ]
> > O1 OH -0.432600 1
> > C1 CT 0.130400 2
> > C2 CT 0.127400 3
> > H1 H1 0.042700 4
> > H2 H1 0.042700 5
> > H3 H1 0.035700 6
> > H4 H1 0.035700 7
> > OS OH -0.603301 8
> > HS HO 0.405000 9
> >
> > [ bonds ]
> > O1 C1
> > C1 C2
> > C1 H1
> > C1 H2
> > C2 H3
> > C2 H4
> > C2 OS
> > OS H5
> > -C2 O1
> >
> > I also tried with gromacs 5, but I got the same error.
> >
> > On 8/24/16, SAKO MIRZAIE <sako.biochem at gmail.com> wrote:
> >> sorry, I made a mistake, the output is mdout.mdp. maybe I should try
> >> the gromacs 5. I also tried to run a martini md on it. but when I
> >> employed polarize water, in minimization step, I got a lot of LINKS
> >> errors. now, I come back to atomistic md, and hope to solve it.
> >>
> >>
> >>
> >> On 8/24/16, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> >>> 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
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> >>>> posting!
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> 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
> >>>>
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> >>>> 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/
> >
>
>
> --
> ***********************************************
> 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
>
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