Dear Mark<br><br>thanks for your reply<br><br>you said &quot;if pdb2gmx is able to treat the whole system in one pass, then it will write such position restraint<br>files automatically&quot;<br><br>in my system, what pdb2gmx includes are in below:<br>
<br>; Include forcefield parameters<br>#include &quot;amber03.ff/forcefield.itp&quot;<br><br>; Include chain topologies<br>#include &quot;complex_Protein_chain_A.itp&quot;<br>#include &quot;complex_DNA_chain_B.itp&quot;<br>
<br>; Include Position restraint file<br>#ifdef POSRES<br>#include &quot;posre_Protein_chain_A.itp&quot;<br><br>; Include Position restraint file<br>#ifdef POSRES<br>#include &quot;posre_Protein_chain_B.itp&quot;<br><br>; Include water topology<br>
#include &quot;amber03.ff/tip3p.itp&quot;<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 &quot;amber03.ff/ions.itp&quot;<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&#39;t know about step 1.<br><br>please guide me about that.<br>