Hello justin ,<br><br>thanks for ur previous suggestion . I am doing simulation of membrene protein , as u suggest in previous mail to use gromos9653a6 forcefield parameters in topology file of protein+lipid bilayer.<br>
I have made topology accordingly like this-<br><br>; Include forcefield parameters <br>#include "ffG53a6.itp"<br>#include "lipid.itp"<br>#include "dmpc.itp" <br><br>; Include chain topologies<br>
#include "rr1_A.itp"<br>#include "rr1_B.itp"<br><br>; Include position restrain protein<br>;#ifdef POSRES_PROTEIN<br>;#include "posre_A.itp"<br>;#include "posre_B.itp"<br>;#endif<br>
<br>; Include position restrain lipid<br>;#ifdef POSRES_LIPID<br>;#include "lip_posre.itp<br>;#endif<br><br>; Include water topology<br>#ifdef FLEX_SPC<br>#include "flexspc.itp"<br>#else<br>#include "spc.itp"<br>
#endif<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 generic topology for ions<br>
#include "ions.itp"<br><br><br>[ system ]<br>; Name<br>PROTEIN IN DMPC BILAYER + WATER <br><br>[ molecules ]<br>; compound #mols<br>Protein_A 1<br>Protein_B 1<br>DMPC 128<br>SOL 3552<br>Na 1<br>
<br>But when I run the grompp command I got the error like this- <br>Fatal error:<br>Atomtype CA not found<br><br>I have tried to solve this problem by adding CA atom with its mass in ffG53a6.atp file and atom CA with its all information ffG53a6nb.itp file but even after doing this correction I am getting same error .<br>
Please Can u suggest me what should I have to do to solve this problem .<br><br>I am a new gromacs user , I have done the simulation of protein and lipid bilayer separetly but this type of problem didnot came so I have no much idea .<br>
I am waiting for ur reply.<br><br>NITU SHARMA<br>SCHOOL OF LIFE SCIENCES<br>JAWAHERLAL NEHRU UNIVERSITY<br>NEW DELHI, INDIA<br>