On 10/01/2012 10:46 PM, Steven Neumann wrote:
Thank you. Imagine I would like to put ligands in further simulations. Should I then copy coordinates of my ligands in smaller box (not to overlap my tube) and then copy both coordinates of ions and ligands plus protein?
Any way you want to construct your non-overlapping non-solvent non-ion molecules is fine. Previous EM of each is wise, but not necessarily required - vacuo EM is probably fine. Then solvate, then use genion, then EM the whole system. Copying ions from earlier calculations is a good way to generate atomic clashes, which is a high price to pay for randomly-placed ions that are different from those generated as above.
Mark
On Tue, Jan 10, 2012 at 11:31 AM, Mark Abraham <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:On 10/01/2012 10:13 PM, Steven Neumann wrote: Thank you. Should I also copy and paste coordinates of my ions or just my protein? The randomly-placed ions will be immaterial for EM. Mark-- gmx-users mailing list gmx-users@gromacs.org<mailto: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 <mailto: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
