[gmx-users] unknown bond atom_type +

SAKO MIRZAIE sako.biochem at gmail.com
Wed Aug 24 01:24:43 CEST 2016


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
>>> >
>>> > * 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.
>>>
>>
>
>
> --
> ***********************************************
> 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/


More information about the gromacs.org_gmx-users mailing list