You are right Peter 2012/5/21 Peter C. Lai <[email protected]>
> This approach still requires the system to be parameterized as a single > moleculetype, doesn't it? > > On 2012-05-20 04:42:26PM +0200, francesco oteri wrote: > > Hi, > > if you are able to define atom couples able to mantein the structure of > > your complex, > > you can insert in .top file a set of bond using function 6 (see table at > > pag 125 of the user manual). > > For example, let atom 1 and 100 are at distance 0.6nm, you can insert in > > .top a row like > > > > 1 100 6 0.6 1000 > > > > you impose a bond between the two atoms having as eauilibrium distance > > 0.6nm and > > force strenght 1000J. > > > > Function 6 doesn't implie the generation of angles and dihedrals so it is > > the right choice > > to impose distance restraints > > > > > > Francesco > > 2012/5/20 R.S.K.Vijayan <[email protected]> > > > > > 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 <[email protected]> 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 [email protected] > > >> > 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 [email protected]. > > >> > 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 > > >> [email protected] | Birmingham AL 35294-4461 > > >> (205) 690-0808 | > > >> ================================================================== > > >> > > >> -- > > >> gmx-users mailing list [email protected] > > >> 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 [email protected]. > > >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > > > > > > > > -- > > > gmx-users mailing list [email protected] > > > 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 [email protected]. > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > -- > > Cordiali saluti, Dr.Oteri Francesco > > > -- > > gmx-users mailing list [email protected] > > 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 [email protected]. > > 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 > [email protected] | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Cordiali saluti, Dr.Oteri Francesco
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