May I upload my input and output files? solving this problem is really critical for me.
thanks, On 8/24/16, SAKO MIRZAIE <sako.bioc...@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.bioc...@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.abra...@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.bioc...@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.abra...@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.bioc...@gmail.com> >>>> > wrote: >>>> > >>>> >> Dear Mark, >>>> >> >>>> >> what do you think about my problem? >>>> >> >>>> >> best regards, >>>> >> >>>> >> On 8/24/16, SAKO MIRZAIE <sako.bioc...@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.abra...@gmail.com> wrote: >>>> >> >> Hi, >>>> >> >> >>>> >> >> The full version, I should say. >>>> >> >> >>>> >> >> Mark >>>> >> >> >>>> >> >> On Tue, 23 Aug 2016 23:54 Mark Abraham <mark.j.abra...@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.bioc...@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-requ...@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-requ...@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-requ...@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 * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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