> Hellow: > I have a protein which have 4 calcium ions binding sites,Now I have > the free > calcium ions protein, I want to add calcium ions on the binding sites,but > I know > the free ions protein conformation is very different to ions loaded > protein. So I > want to know whether there is some way to let complex of protein and ions > to a > native ca2+ loaded conformation.
You need to choose a force field that you think has some prospects of modelling the ion-loading sites. Then you need to build a reasonable starting structure using your chemical knowledge and your favourite molecule builder - or even hacking them into a structure file by hand. Then feed that to pdb2gmx and tweak things to get the ions recognised as part of the molecule and the interactions all what you want. Then you need to hope that you can relax from the unloaded structure to the loaded structure in an MD-accesible time frame - or to hack the structure yourself to achieve that. These are not simple operations, and I would not recommend this task as a first exercise in non-trivial MD and/or tweaking protein topologies. Beware! Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
