Many thanks for your response. No special reasons for parametrizing the ligand and the protein as a separate system. I dont think that the ligand and protein can be parametrized as a single system, but will definitely try doing it as a single system and see if it works. Regards Vijayan.R
On Sat, May 19, 2012 at 10:23 PM, Peter C. Lai <p...@uab.edu> wrote: > Is there a particular reason why the ligand has been parameterized as a > separate moleculetype from the protein in your case? I prefer to treat > coordination bonds as "real bonds" instead of relying on electrostatic > interactions anyway, since it is the only way to conservatively ensure the > coordination geometry is preserved (like for Zn, where QM predicts a > tetrahedral geometry but Zn free ions will result in an octahedral > geometry). > In any case, even if you stick with freeion Zn, you can paramaterize the > complex as a single moleculetype and use distance restraints there, can't > you? > > > On 2012-05-19 09:42:25PM -0400, R.S.K.Vijayan wrote: > > Dear Gromacs users > > > > I was wondering if there exists any technique that sets > > distance restraint between specified ligand (atoms) and the > protein(atoms) > > in Gromacs. I am simulating a system which contains metal ions > coordinated > > to the Ligand. I looked in to the mailing list and Gromacs manual and > > figured out that *genrster* can be employed, to > > set distance, position and dihedral restraints. Unfortunately i also > > stumbled on the fact that restraints between systems is not possible. > > > > Since force fields are not good at handling chelation between metal > atoms, > > i find that the metals drifting away from the coordinated ligand atoms > > during the course of simulation, hence i introduced position constraints > > for the metal and ended up realizing that the coordination distance > > between the ligand and the metal exceeds the permissible range and the > > angles between the chelating atoms gets distorted and some coordinating > > residues like Histidine and Aspartic acid also moves away from the > metal. > > > > Hence, i was wondering if l anyone knows of any method (apart from > > QM/MM) that can help to set distance restraints between the protein > (metal > > ion ) and the ligand, also any suggestion that could help in handling > > ligand metal chelation is welcomed. > > Thanking in advance > > > > > > Regards > > > > Vijayan.R > > > -- > > 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 > > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > 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