This tutorial doesn't seem to be quite useful, if so many errors pop up. Maybe it was implemented for Gromacs < 4.5.x but there's no info on the version it should be used.
However, Lo and behold! I found that you have a nice page with Gromacs 4.5.x tutorials :D ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html) I'll give a try with the Lyzosyme one! - Jose On Wed, Dec 7, 2011 at 1:29 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Jose Borreguero wrote: > >> Hi Justin, thanks for your reply! >> >> I appended '-p protein.top' to genion. File protein.top was automatically >> updated by insertion of the following lines at the end of the file: >> /[ molecules ] >> >> ; Compound #mols >> Protein_chain_A 1 >> SOL 7791 >> NA+ 26 >> CL- 23/ >> >> >> My solvated PDB, protein-solvent.pdb contains lines like these: >> ATOM 24543 NA NA+ 8043 50.712 66.452 12.341 1.00 0.00 >> >> Now when I run grommp, I get the error >> /Fatal error: >> No such moleculetype NA+/ >> >> >> I checked file gromos45a3.ff/ions.itp. The sodium is included in this >> fashion: >> /[ moleculetype ] >> >> ; molname nrexcl >> NA 1 >> [ atoms ] >> ; id at type res nr residu name at name cg nr charge mass >> 1 NA+ 1 NA NA 1 22.9898/ >> >> >> It seems the naming convention of ions.itp is different than that of >> protein.top and protein-solvent.pdb. I changed protein.top and >> > > What was your exact genion command? If you tell genion to use "-pname > NA+" (which is wrong) you get this result. Note that the error says the > moleculetype "NA+" is not found; the moleculetype name is "NA" instead. > > protein-solvent.pdb to match the naming of ions.itp. Then when I run >> grompp I get the error: >> /ERROR 1 [file protein.top, line 7228]: >> >> ERROR: One of the box lengths is smaller than twice the cut-off length. >> Increase the box size or decrease rlist./ >> >> The puzzling thing is that line 7228 of protein.top is the last line of >> the file, that is, >> CL 23 >> So the error message is not much help :( >> > > The problem comes from the coordinate file and settings of the .mdp file; > they are somehow incompatible such that they would cause a violation of the > minimum image convention. Why the error points to the .top I cannot say. > > > -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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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