Thank you for your suggestions. I have checked the topology file with vim, and it looks pefectly, also, the only problem happens when I use genion. One thing that might be possible is that I use the double precision version of gromacs, because when I solve it in water, the written of topology file looks weired(like I showed). What do you mean by work-around? You mean just manually change some water molecules in topology file and coordinate file into ions? Will the program recognize something like CL, NA? Or can I just add ions to the system and solve it in water?
Thank you very much Best Wishes Ye 2011/6/16 Justin A. Lemkul <jalem...@vt.edu> > > > Ye Yang wrote: > >> Hi, everyone: >> I am a new user of Gromacs, and I am running through the tutorial. >> When I am trying to run the ligand-receptor binding tutorial from >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html >> I met some trouble in adding ion. >> Each time when I use genion, it shows: >> >> Will try to add 0 NA ions and 6 CL ions. >> Select a continuous group of solvent molecules >> Group 0 ( System) has 33046 elements >> Group 1 ( Protein) has 1693 elements >> Group 2 ( Protein-H) has 1301 elements >> Group 3 ( C-alpha) has 163 elements >> Group 4 ( Backbone) has 489 elements >> Group 5 ( MainChain) has 653 elements >> Group 6 ( MainChain+Cb) has 805 elements >> Group 7 ( MainChain+H) has 815 elements >> Group 8 ( SideChain) has 878 elements >> Group 9 ( SideChain-H) has 648 elements >> Group 10 ( Prot-Masses) has 1693 elements >> Group 11 ( non-Protein) has 31353 elements >> Group 12 ( Other) has 15 elements >> Group 13 ( JZ4) has 15 elements >> Group 14 ( Water) has 31338 elements >> Group 15 ( SOL) has 31338 elements >> Group 16 ( non-Water) has 1708 elements >> Select a group: 15 >> Selected 15: 'SOL' >> Number of (3-atomic) solvent molecules: 10446 >> >> Processing topology >> >> Back Off! I just backed up temp.top to ./#temp.top.3# >> >> ------------------------------------------------------- >> Program genion_d, VERSION 4.5.4 >> Source code file: gmx_genion.c, line: 285 >> >> Fatal error: >> No line with moleculetype 'SOL' found the [ molecules ] section of file >> 'topol.top' >> >> > Something doesn't match up here - the command backs up temp.top, but then > complains it can't find SOL in topol.top. Either genion is looking at the > wrong file or your command is somehow wrong. > > > I checked my topology file and it looks fine: >> ; Include Position restraint file >> #ifdef POSRES >> #include "posre.itp" >> #endif >> >> ; Include water topology >> #include "gromos43a1.ff/spc.itp" >> >> ; Include ligand topoloty >> #include "drg.itp" >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 1 1 1000 1000 1000 >> #endif >> >> ; Include topology for ions >> #include "gromos43a1.ff/ions.itp" >> >> [ system ] >> ; Name >> >> Protein >> [ molecules ] >> ; Compound #mols >> Protein_chain_A 1 >> JZ4 1 SOL 10446 >> >> One thing that might happen is in the genion source file, I read through >> it, and the problem either happens in loading the line to buf2, or in the >> gmx_strcmp(buf2,"SOL"), since clearly the SOL_line is -1 aftermath. >> >> The other thing I tried is to remove the ligand JZ4 part in both topology >> and coordinates file, and in this case, it works perfectly for adding ion. >> But in this way, I do not know how to insert my ligand into the system since >> it might collide with solvent. >> >> > If removal of the JZ4 line relieves the problem, perhaps there's a problem > with that line, i.e. the line ending? What type of system are you using? > Sometimes Windows line endings cause problems. Always use a plain text > editor and use dos2unix to process text files if you're on Windows. > > Otherwise, the work-around is to not have genion work on the topology. > Make the corrections yourself. Simple addition of ions and subtraction of > water molecules is trivial. > > -Justin > > > Can someone help me with this problem? >> >> Thank you all very much. >> >> Ye Yang >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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