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.dun...@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 part of the tutorial) except that the line 'pbc = no' has been replaced by 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-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. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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
