Hi Vitaly, This is after runing genbox: ----------------------------------- opening library file /home/seyedyazdij/gromacs-4.0.5/share/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /home/seyedyazdij/gromacs-4.0.5/share/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /home/seyedyazdij/gromacs-4.0.5/share/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /home/seyedyazdij/gromacs-4.0.5/share/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /home/seyedyazdij/gromacs-4.0.5/share/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /home/seyedyazdij/gromacs-4.0.5/share/top/elements.dat Entries in elements.dat: 218 Reading solute configuration Fullereno in vacuum Containing 60 atoms in 1 residues Initialising van der waals distances... Reading solvent configuration "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984" solvent configuration contains 648 atoms in 216 residues
Initialising van der waals distances... Will generate new solvent configuration of 1x1x1 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 216 residues Calculating Overlap... box_margin = 0.315 Removed 528 atoms that were outside the box Neighborsearching with a cut-off of 0.45 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45 System total charge: 0.000 ------------------------------------------------------- Program genbox, VERSION 4.0.5 Source code file: ns.c, line: 2295 Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. ------------------------------------------------------- Thanks in advance/Jamie On Thu, Aug 13, 2009 at 2:10 PM, Vitaly V. Chaban <vvcha...@gmail.com>wrote: > What is the box size and what is the cutoff displayed by genbox? > > On Thu, Aug 13, 2009 at 8:10 PM, Jamie Seyed<jamie.se...@gmail.com> wrote: > > Hi Vitaly, > > Thanks for the answer. When I said far away means my pore was in one > corner > > of vmd window and the water molecules in opposite corner (almost). > Anyways, > > I tried to use your method but I think I am missing some parts... > > I did: > > (1)editconf -bt cubic -f conf.gro -o pore_edco.pdb -d 0.02 ---> seems > fine > > (2)genbox -cp pore_edco.pdb -cs spc216.gro -o pore edco_b4em.pdb -p > > topol.top here there is an error: one of the box vectors has become > shorter > > than twice the cut-off length or box_yy-|box_zy| or box_zz has become > > smaller than the cut-off. > > > > would you please let me know how I can fix the error (I don't see where I > > can change the cut-off !). Also am I doing right or I need a box of water > > first without introducing my molecule... > > I appreciate to get more information and some help... Thanks a lot/Jamie > > > > > > On Thu, Aug 13, 2009 at 12:21 PM, Vitaly V. Chaban <vvcha...@gmail.com> > > wrote: > >> > >> Jamie, > >> > >> I didn't understand why you meant saying "waters far from the outside > >> of the pore"... Far from outside, then where exactly? Maybe I just > >> imagine your box incorrectly. > >> > >> To fill the pore with a solvent try to "deceive" genbox a little: > >> 1) make a box (see editconf) in such a way that it contains only > >> "inside" part of your pore. genbox will not report an error from its > >> side. > >> 2) add the solvent with genbox. > >> 3) return to the original box size. > >> 4) add the outside part. > >> > >> Vitaly > >> > >> > I want to know how can I use genbox to fill inside of the pore as well > >> > as a > >> > layer outside. From the "man genbox" page I try to use -shell with a > >> > negative value (?) but it put waters far from the outside of the pore > >> > and I > >> > think it does not care about the sign. It seems strange to me because > >> > when I > >> > had 10 10 10 in the last line of my f.gro, by a shell 0.5 or 0.2, I > got > >> > a > >> > layer of few molecule around the pore, but when I change it to 1. 1. > 1., > >> > the > >> > water molecules generated far away. I appreciate if someone tell me > (1) > >> > how > >> > I can add water inside the pore and (2) why changing the box size will > >> > give > >> > a opposite result. Please advise..Thanks in advance/Jamie > _______________________________________________ > 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 >
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