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