Re: [gmx-users] Trouble with Gromacs finding the files it needs
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 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 listgmx-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
Re: [gmx-users] Trouble with Gromacs finding the files it needs
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
Re: [gmx-users] Trouble with Gromacs finding the files it needs
J. Nathan Scott wrote: snip 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. There's no problem. That's a default name specified in src/gmxlib/string2.c that is used in place of other parameters if they are not available. -Justin -- 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 listgmx-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
Re: [gmx-users] Trouble with Gromacs finding the files it needs
Hi all, I believe onbekend is Dutch for unknown. Rogan On Nov 30, 2010, at 3:54 PM, Justin A. Lemkul wrote: J. Nathan Scott wrote: snip 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. There's no problem. That's a default name specified in src/gmxlib/ string2.c that is used in place of other parameters if they are not available. -Justin -- 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 listgmx-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 -- gmx-users mailing listgmx-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
