On Tue, Nov 30, 2010 at 2:13 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > J. Nathan Scott wrote: >> >> Hello Gromacs users, >> >> I am having some difficulties with Gromacs finding the files it needs >> (at least that is what I *think* is the problem) and am hoping that >> someone can offer some insight. Using another user's home directory >> installation of Gromacs (v 4.0.7) I was able to work my way through >> Justin Lemkul's very nice lysozyme tutorial. However, now that I am >> working from my own home directory installation of Gromacs (v 4.5.3) I >> keep running into problems involving the addition of chloride ions in >> that same tutorial (as well as in other applications). The error I'm >> receiving using the newer version and installation of Gromacs occurs >> when I am using grommp to prepare a file containing protein, solvent, >> and ions for energy minimization: >> ------------------------------------------------------- >> Program grompp, VERSION 4.5.3 >> Source code file: toppush.c, line: 1987 >> >> Fatal error: >> No such moleculetype CL- >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> ------------------------------------------------------- >> >> This is very confusing since all I am doing is using a newer >> installation of Gromacs and following the exact same commands from the >> tutorial. Naturally I started checking and comparing topology files >> from the 2 runs to see if I could figure out what was going on. I >> noticed a few differences but am unsure what to make of them. >> >> The older version of Gromacs, for instance, has the user and host >> names correct at the top of the topology file, whereas my freshly >> installed version has both user and host as "onbekend", so it seems >> that user and host information is not being communicated in my new >> copy of Gromacs. Also, the topology file generated by the older >> version has includes of the form of #include "ffoplsaa.itp", #include >> "posre.itp", #include "spce.itp", and #include "ions.itp" whereas the >> newer version has includes of the form #include >> "oplsaa.ff/forcefield.itp", #include "posre.itp", #include >> "oplsaa.ff/spce.itp", and #include "oplsaa.ff/ions.itp". >> >> I know of course that "CL-" is the correct form of the chloride ion in >> OPLSAA (I checked oplsaa.ff/ions.itp to be certain), so I am quite >> baffled as to why this error is occurring. Is this indeed some sort of >> path problem, perhaps? I have noted that when I use "CL" instead of >> "CL-" in genion grommp has no trouble, but I believe it *should* >> because I have selected the OPLSAA forcefield. I have also noted that >> when I replace "oplsaa.ff/ions.itp" in my topology file with just >> "ions.itp" grommp runs fine, but this worries because I don't know why >> it works. >> > > The directory structure has changed as of version 4.5, and ion names have > been standardized across the force fields. The proper [moleculetype] of the > chloride ion (in oplsaa.ff/ions.itp) is indeed "CL" while the *residue name* > is "CL-" and the atom name (which is what you pass to genion) is "CL." > > So, if you have added a line like > > CL- 8 > > in the [molecules] directive of your topology (like in my tutorial), then > you get the fatal error. The [moleculetype] name is what you enter here, > not the residue name. > > I haven't updated my tutorial for version 4.5.x, but perhaps I should. If > you follow what I say exactly, you will have problems in the newer version. > > -Justin >
Ahhh, now it all makes sense! Thanks very much for your helpful answer Justin! By the way, should I be concerned about "onbekend" in the user and server names? I don't particularly care what is in those fields, but am slightly worried that they indicate I have something configured incorrectly, which could then affect the functionality of the software. -Nathan >> In case it makes any difference, I installed Gromacs using the >> following procedure to yield MPI single and double precision versions >> of mdrun and single and double precision non-MPI versions of the >> tools: >> >> ./configure --enable-mpi --disable-float --prefix=/home/scott/gromacs >> --program-suffix=_mpi_d >> make mdrun && make install-mdrun >> make distclean >> >> ./configure --enable-mpi --enable-float --prefix=/home/scott/gromacs >> --program-suffix=_mpi >> make mdrun && make install-mdrun >> make distclean >> >> ./configure --disable-float --prefix=/home/scott/gromacs >> --program-suffix=_d >> make && make install >> make distclean >> >> ./configure --enable-float --prefix=/home/scott/gromacs >> make && make install >> >> Thank you very much for any help you can provide, this problem really >> has me scratching my head! >> >> ---------- >> J. Nathan Scott, Ph.D. >> Postdoctoral Fellow >> Department of Chemistry and Biochemistry >> Montana State University > > -- > ======================================== > > 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-us...@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 > ---------- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- 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