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/ -- 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.