Re: [gmx-users] How to avoid adding ions close to ligand
There is nothing stopping you from replacing the ion in your binding pocket with the original water and then replacing another water elsewhere with the ion at the oxygen's coordintes, then running genconf to renumber the gro file. On 2012-11-26 06:25:47PM -0800, Yun Shi wrote: > I did hope the ions will move out eventually. > > But after my ~70ns of conventional MD (with duplicate MD runs and the > protein as a dimer with identical sequence), they were still there in > the binding site. > > So I assume it would be much better to start without any salt ions > beside my ligand. > > Could anyone suggest a way around this? > > Thanks, > Yun > > On Mon, Nov 26, 2012 at 12:39 PM, David van der Spoel > wrote: > > On 2012-11-26 21:28, Yun Shi wrote: > >> > >> Hi everyone, > >> > >> I am doing conventional MD of a protein-ligand system with a mobile > >> loop as part of the binding site. > >> > >> Presumably, the positive Arg side chain on the mobile loop will > >> eventually move towards the negative carboxylic group on my ligand. > >> But I found the addition of NaCl (0.15 M conc.) had some effect on > >> this movement, since the random addition could put Na+ or Cl- ions > >> between the mobile loop and my ligand. > >> > >> I tried generating a index containing only SOL far not close to my > >> ligand, but apparently genion requires a continuous solvent group. So > >> is there any other way to achieve this? Trying different numbers for > >> -seed option seems inefficient and is dependent on luck. > >> > >> Thanks, > >> Yun > >> > > Maybe your assumption is wrong? > > > > Run a long MD simulation and you will find out. > > > > -- > > David van der Spoel, Ph.D., Professor of Biology > > Dept. of Cell & Molec. Biol., Uppsala University. > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > > -- > > gmx-users mailing listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] How to avoid adding ions close to ligand
I did hope the ions will move out eventually. But after my ~70ns of conventional MD (with duplicate MD runs and the protein as a dimer with identical sequence), they were still there in the binding site. So I assume it would be much better to start without any salt ions beside my ligand. Could anyone suggest a way around this? Thanks, Yun On Mon, Nov 26, 2012 at 12:39 PM, David van der Spoel wrote: > On 2012-11-26 21:28, Yun Shi wrote: >> >> Hi everyone, >> >> I am doing conventional MD of a protein-ligand system with a mobile >> loop as part of the binding site. >> >> Presumably, the positive Arg side chain on the mobile loop will >> eventually move towards the negative carboxylic group on my ligand. >> But I found the addition of NaCl (0.15 M conc.) had some effect on >> this movement, since the random addition could put Na+ or Cl- ions >> between the mobile loop and my ligand. >> >> I tried generating a index containing only SOL far not close to my >> ligand, but apparently genion requires a continuous solvent group. So >> is there any other way to achieve this? Trying different numbers for >> -seed option seems inefficient and is dependent on luck. >> >> Thanks, >> Yun >> > Maybe your assumption is wrong? > > Run a long MD simulation and you will find out. > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > -- > gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] How to avoid adding ions close to ligand
On 2012-11-26 21:28, Yun Shi wrote: Hi everyone, I am doing conventional MD of a protein-ligand system with a mobile loop as part of the binding site. Presumably, the positive Arg side chain on the mobile loop will eventually move towards the negative carboxylic group on my ligand. But I found the addition of NaCl (0.15 M conc.) had some effect on this movement, since the random addition could put Na+ or Cl- ions between the mobile loop and my ligand. I tried generating a index containing only SOL far not close to my ligand, but apparently genion requires a continuous solvent group. So is there any other way to achieve this? Trying different numbers for -seed option seems inefficient and is dependent on luck. Thanks, Yun Maybe your assumption is wrong? Run a long MD simulation and you will find out. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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
