[gmx-users] unknown bond atom_type +
SAKO MIRZAIE
sako.biochem at gmail.com
Wed Aug 24 01:27:08 CEST 2016
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
>>>> > 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/
>>>> --
>>>> 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/
>
--
***********************************************
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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