Hi, > I tried to solvate an assembly of amyliod peptides (16 peptide), using > editconf and genbox respectively as follow, > editconf -f rotated.gro -box 76 6 6 -center 0 0 0 -o rotated-box > > Nothing here does any rotation.
Well, it seems something that was rotated goes in... that seems fine. > Sounds like the combination of your input coordinates, specification of the > center and box sizes places the protein outside the box. The specification of -center 0 0 0 will result in the center of geometry of your chains to be placed at the origin. Your box will start at the origin, so doing this by definition will place the majority of your system outside of the box. Then again, if you process it like you would for simulation, you will find it doesn't matter, as there is no outside out of the box. > So, what do you suggest? Read more, in particular regarding periodic boundary conditions and go on with the next step in your protocol. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials 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/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
