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