Dear all, I want to apply distance restraint between Zn and its coordinating atoms. Zn is supposed to be in octahedral geometry. Zn is making coordination bond with O of hydroxyl group in ligand atom also. Even after several attempts, it seems like destance restraint is not effective because after 1ns MD run, ligand and Zn both move away from their position in opposite directions.
I have put following lines in mdp file: title = Protein-ligand complex define = -DPOSRESLIG ; distance restrain from metal disre = simple and added following lines into .top file ; Include Position restraint file #ifdef POSRESLIG #include "metalposre.itp" #endif where metalporse.itp contains 671 11637 1 3 1 0.09 0.192 0.29 1 4059 11637 1 7 1 0.11 0.21 0.31 1 4070 11637 1 10 1 0.096 0.196 0.296 1 4071 11637 1 12 1 0.094 0.195 0.295 1 11637 11662 1 14 1 0.12 0.23 0.32 1 where 671 -> OD2 of Asp45, 4059 -> NE2 of Hid267, 4070 -> OD1 of Asp268, 4071 -> OD2 of Asp268, 11637 -> Zn and 11662 -> O of Lig. looking for suggestions. Thank you Priyanka Shah Central Drug Research Institute Lucknow, India -- Let spontaneity guide you! -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
