-- Xianqiang Sun Email: xianqi...@theochem.kth.se Division of Theoretical Chemistry and Biology School of Biotechnology Royal Institute of Technology S-106 91 Stockholm, Sweden At 2012-01-04 04:04:46,"Justin A. Lemkul" <jalem...@vt.edu> wrote: > > >xianqiang wrote: >> You do not need to fix the copper in the calculation. There are must be >> some negative charged residues around the copper. Therefore, the copper >> will located at the place where it should be. >> > >I agree that a position restraint on copper is not appropriate, but I strongly >disagree with the assumption that it will simply be held in place by virtue of >negative charges. I know of many cases where the MM approximations and >electrostatic interactions were insufficient to preserve active-site geometry. >There are a number of QM/MM studies that have concluded that fixed point >charges >on such species suffer from many limitations, not the least of which are >inductive effects and the inability to account for orbital geometry. A series >of distance restraints between ligating residues and the copper ion itself may >be the best approach for "standard" MD simulations. > >-Justin > >-- >======================================== > >Justin A. Lemkul >Ph.D. Candidate >ICTAS Doctoral Scholar >MILES-IGERT Trainee >Department of Biochemistry >Virginia Tech >Blacksburg, VA >jalemkul[at]vt.edu | (540) 231-9080 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > I agree your opinion on some degree. But I think he should do the simulation with the copper at reasonable place without restraint at first. If it is not work, the electrostatic interaction may be not strong enough for locating the copper. Then, he can redo the calculation with distance restraint between the copper and residues nearby. So the choice should depend on the system he worked on. regards >======================================== >-- >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
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