[gmx-users] unknown bond atom_type +

[SAKO MIRZAIE]

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
>> >>>>
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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/
>>
> --
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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/