Hi everyone, I am currently doing a simulation which involves a dopamine receptor placed in a POPC membrane and an agonist or antagonist in the active site. The ligand was placed by VS and is closed to what the biology gives. My problem is that the ligand get out of is normal position during the simulation. I know it is easier to move the ligand than the receptor but that is not the biological answer. I would like to know if there is a way to fix the ligand so that the receptor would be force to adapt around it and not the inverse. There is know Hbonds with specific amino acid is it possible to add this information in the run.
I tried so far to use position restraint in my ligand.itp [ position_restraints ] ; i funct fcx fcy fcz 1 1 10000 10000 10000 3 1 10000 10000 10000 4 1 10000 10000 10000 5 1 10000 10000 10000 6 1 10000 10000 10000 8 1 10000 10000 10000 9 1 10000 10000 10000 10 1 10000 10000 10000 11 1 10000 10000 10000 12 1 10000 10000 10000 13 1 10000 10000 10000 But it didn't have any effect on the final MD simulation of 10 ns. At the end the ligand was completely out of the site. Could anyone help me? Thank you in advance Sabine _______________________________________________ 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/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/mailing_lists/users.php