Thanks for your reply Mr.justin<br>i am sending the commands and .itp file sequence<br>the command i have used for protein insertion into membrane is <br>genbox -cs lipid.gro -cp protein.gro -p topol.top -o popc_protein.gro , this command was fine it ran without error. <br>
Later<br>grompp -f em.mdp -c popc_protein.gro(generated by genbox) -p topol.top (generated by genbox) -o em.tpr<br>when i ran this grompp command its showing that atom typr NR, HC, CR1 not found<br> i am pasting part of my topology file<br>
<br> This is your topology file<br>; "Move Over Hogey Bear" (Urban Dance Squad)<br>;<br>; Include forcefield parameters<br>#include "ffgmx.itp"<br>#include "lipid.itp"<br>#include "popc.itp<br>
<br><br>17 N 3 HISH N 7 -0.28 14.0067 ; qtot 0.72<br> 18 H 3 HISH H 7 0.28 1.008 ; qtot 1<br> 19 CH1 3 HISH CA 8 0 13.019 ; qtot 1<br>
20 CH2 3 HISH CB 8 0 14.027 ; qtot 1<br> 21 C 3 HISH CG 9 -0.05 12.011 ; qtot 0.95<br> 22 NR 3 HISH ND1 9 0.38 14.0067 ; qtot 1.33<br>
23 H 3 HISH HD1 9 0.3 1.008 ; qtot 1.63<br> 24 CR1 3 HISH CD2 9 0 13.019 ; qtot 1.63<br> 25 CR1 3 HISH CE1 9 -0.24 13.019 ; qtot 1.39<br>
26 NR 3 HISH NE2 9 0.31 14.0067 ; qtot 1.7<br> 27 H 3 HISH HE2 9 0.3 1.008 ; qtot 2<br> 28 C 3 HISH C 10 0.38 12.011 ; qtot 2.38<br>
29 O 3 HISH O 10 -0.38 15.9994 ; qtot 2<br> 30 N 4 HISH N 11 -0.28 14.0067 ; qtot 1.72<br> 31 H 4 HISH H 11 0.28 1.008 ; qtot 2<br>
32 CH1 4 HISH CA 12 0 13.019 ; qtot 2<br> 33 CH2 4 HISH CB 12 0 14.027 ; qtot 2<br> 34 C 4 HISH CG 13 -0.05 12.011 ; qtot 1.95<br>
35 NR 4 HISH ND1 13 0.38 14.0067 ; qtot 2.33<br> 36 H 4 HISH HD1 13 0.3 1.008 ; qtot 2.63<br> 37 CR1 4 HISH CD2 13 0 13.019 ; qtot 2.63<br>
38 CR1 4 HISH CE1 13 -0.24 13.019 ; qtot 2.39<br> 39 NR 4 HISH NE2 13 0.31 14.0067 ; qtot 2.7<br> 40 H 4 HISH HE2 13 0.3 1.008 ; qtot 3<br>
41 C 4 HISH C 14 0.38 12.011 ; qtot 3.38<br> 42 O 4 HISH O 14 -0.38 15.9994 ; qtot 3<br><br>366 N 41 PHE N 160 -0.28 14.0067 ; qtot 2.72<br>
367 H 41 PHE H 160 0.28 1.008 ; qtot 3<br> 368 CH1 41 PHE CA 161 0 13.019 ; qtot 3<br> 369 CH2 41 PHE CB 161 0 14.027 ; qtot 3<br>
370 C 41 PHE CG 161 0 12.011 ; qtot 3<br> 371 C 41 PHE CD1 162 -0.1 12.011 ; qtot 2.9<br> 372 HC 41 PHE HD1 162 0.1 1.008 ; qtot 3<br>
373 C 41 PHE CD2 163 -0.1 12.011 ; qtot 2.9<br> 374 HC 41 PHE HD2 163 0.1 1.008 ; qtot 3<br> 375 C 41 PHE CE1 164 -0.1 12.011 ; qtot 2.9<br>
376 HC 41 PHE HE1 164 0.1 1.008 ; qtot 3<br> 377 C 41 PHE CE2 165 -0.1 12.011 ; qtot 2.9<br> 378 HC 41 PHE HE2 165 0.1 1.008 ; qtot 3<br>
379 C 41 PHE CZ 166 -0.1 12.011 ; qtot 2.9<br> 380 HC 41 PHE HZ 166 0.1 1.008 ; qtot 3<br> 381 C 41 PHE C 167 0.38 12.011 ; qtot 3.38<br>
382 O 41 PHE O 167 -0.38 15.9994 ; qtot 3<br><br>; Include Position restraint file<br>#ifdef POSRES<br>#include "posre.itp"<br>#endif<br><br>; Include water topology<br>#include "spc.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 generic topology for ions<br>
#include "ions.itp"<br><br>[ system ]<br>; Name<br>protein in popc in water<br><br>[ molecules ]<br>; Compound #mols<br>Protein 1<br>POPC 98<br>CL- 3<br>
SOL 2457<br>Thanks in advance.<br>