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/ -- 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.