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
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