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.