[gmx-users] unknown bond atom_type +

[SAKO MIRZAIE]

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
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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/
>> >>
>> > --
>> > 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/
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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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/