Mark, I've found a possible sollution to restrict oxygens of my X-ray water by possible plasing the below string in the TOPOLOGY.top of my system
; Include X-ray water topology #include "XW.itp" ; Include Position restraint file #ifdef POSRES_XW [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif I havent recieved any errors from gromp. Does this aproach correct in general ? I dont know why but after minimisation constrained mollecules were diffused from the protein interious so POSRES have not worked :( My minim.mdp consist of two separate posres for water as well as for ligand groups ( there are no posre for protein). define = -DPOSRES_LIG -DPOSRES_XW ; position restrain the protein integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform energygrps = Protein CAR What should I add to that file to activate posres? Finally are the constraints algorithm needed here ? James
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