Hi Nayef, Can you
- copy-paste the sequence of commands as you have typed them in (not as you think you typed them in or as they're given in the tutorial) - provide the output of 'tail 1qlz-water.gro' Cheers, Tsjerk On Mon, Jun 21, 2010 at 9:49 PM, Nayef Daher <eltha...@ualberta.ca> wrote: > Hi, > > I have the same problem as listed below back in February. I am using the > latest gromacs version (4.0.7) and tried the solution below by entering > > genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro > > instead of making the output as pdb file. Yet the same result occurs with > the same error message. One of the box lengths is smaller than twice the > cut-off length. > > Please let me know what other options I can try. > > Thanks! > > nayef > ------------------------------------------------------------------------------ > original message below > ------------------------------------------------------------------------------ > > Hi Anna, > > You should mention the version of Gromacs you're using. One of the > versions did not write the box correctly to pdb files, which I think > happened in your case. If you take as the solvation step > > genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro > > instead of writing output to 1qlz-water.pdb, I think you should be fine. > > The reason for writing a .pdb file is the easier visualization with a > multitude of programs. > > Thanks for your interest in the tutorial. > > Cheers, > > Tsjerk > > On Fri, Feb 26, 2010 at 1:27 PM, Anna Duncan > <anna.duncan at mrc-mbu.cam.ac.uk> wrote: >> >> Hi, >> >> I've been trying to go through the 'Introduction to Molecular Dynamics >> Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of the >> tutorials listed on the GROMACS website. >> >> I've got to the stage where I am performing energy minimisation on my >> solvated protein but when I use grompp to create the .tpr file for mdrun, >> I >> get the error message: >> >> One of the box lengths is smaller than twice the cut-off length. Increase >> the box size or decrease rlist >> >> >> I am using the protein with pdb ID 1QLZ, one of the suggested structures >> for >> the tutorial and have so far carried out the following commands: >> >> % pdb2gmx -f 1qlz.pdb -o 1qlz.gro -p 1qlz.top -ignh >> % grompp -f minim.mdp -c 1qlz.gro -p 1qlz.top -o 1qlz-EM-vacuum.tpr >> % mdrun -v -deffnm 1qlz-EM-vacuum.tpr -c 1qlz-EM-vacuum.pdb >> % editconf -f 1qlz-EM-vacuum.pdb -o 1qlz-PBC.gro -bt dodecahedron -d 1.0 >> % genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.pdb >> % grompp -v -f minim.mdp -c 1qlz-water.pdb -p 1qlz.top -o 1qlz-water.tpr >> % genion -s 1qlz-water.tpr -o 1qlz-solvated.pdb -conc 0.15 -neutral -pname >> NA+ -nname CL- >> % grompp -v -f minim_pbc.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o >> 1qlz-EM-solvated.tpr >> >> after which I receive the error message. >> >> The minim_pbd.mdp file I use in the last grompp command is the same as >> minim.mdp used in previous grompp commands (the latter file I downloaded >> as >> part of the tutorial) except that the line 'pbc = no' has been replaced by >> 'pbc = xyz'. >> >> I have tried increasing the value of 'd' in the editconf command, to 2,3 >> and >> even 8 but this doesn't make any difference. (I have read that it is not >> a >> good idea to tamper with the cut-off values so have avoided doing that) >> The >> box vector lengths when d = 1.0 are all 7.10051, and rvdw, rcoulomb = 1.0 >> in >> mimim.mdp and minim_pbd.mdp, so I don't understand what is going wrong... >> >> Anna >> -- >> gmx-users mailing list gmx-users at gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use thewww interface >> or send it to gmx-users-request at gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > Computational Chemist > Medicinal Chemist > Neuropharmacologist > -- > 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/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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/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/mailing_lists/users.php
