Hi, It seems to me that the holes are created by genbox because I don't have them in the original solvent box. The intermediate box (outputed by trjconv) with the protein solvated but not converted is difficult to analyze, because the box doesn't have the right shape and of pbc issues, but it seems to me that the holes are present in this box, i.e. I don't think they are an artifact of trjconv.
Thanks for the help Diana On Sat, Nov 6, 2010 at 8:08 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Diana, > > Yeah, my reply was a bit off, as Vitaly had already pointed out. Lazy > reading, sorry. But are these holes created by genbox, or are they already > present in the acn solven box? Have you already checked all intermediate > structures? > > Cheers, > > Tsjerk > > On Nov 6, 2010 7:25 PM, "Diana Lousa" <dlo...@itqb.unl.pt> wrote: > > Hello, > > No, the hole don't correspond to parts of the protein sticking out on the > other side. The protein is in the center of the box and the holes are not > due to pbc issues. > > > Diana > > On Fri, Nov 5, 2010 at 10:10 PM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > >> > > Hey, > > Do the holes match the parts of the protein sticking out on >> the other side? > > Tsjerk ... >> -- >> >> > gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-u... >> > > > > -- > > Diana Lousa PhD student Protein Modeling Laboratory ITQB/UNL Oeiras, > Portugal > > -- > 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/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 list gmx-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 > -- Diana Lousa PhD student Protein Modeling Laboratory ITQB/UNL Oeiras, Portugal
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