Dear Mark<br><br>thanks for your reply<br><br>you said "if pdb2gmx is able to treat the whole system in one pass, then it will write such position restraint<br>files automatically"<br><br>in my system, what pdb2gmx includes are in below:<br>
<br>; Include forcefield parameters<br>#include "amber03.ff/forcefield.itp"<br><br>; Include chain topologies<br>#include "complex_Protein_chain_A.itp"<br>#include "complex_DNA_chain_B.itp"<br>
<br>; Include Position restraint file<br>#ifdef POSRES<br>#include "posre_Protein_chain_A.itp"<br><br>; Include Position restraint file<br>#ifdef POSRES<br>#include "posre_Protein_chain_B.itp"<br><br>; Include water topology<br>
#include "amber03.ff/tip3p.itp"<br><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>
#endif<br><br>; Include topology for ions<br>#include "amber03.ff/ions.itp"<br><br>[ system ]<br>; Name<br>complex<br><br>[ molecules ]<br>; Compound #mols<br>Protein_chain_A 1<br>DNA_chain_B 1<br>
SOL 3500<br><br><br>unfortunately, I don't know about step 1.<br><br>please guide me about that.<br>