Hi Dear Justin Thanks a lot for your kind answer, I applied two types of command to get rid of the previous error
*at first*, the following command was used: *gmx pdb2gmx -f *.pdb -o *.gro -p topol.top -ignh -water spc * but I confronted these error CYS901 SG7090 1.414 CYS905 SG7117 1.878 0.553 HIS917 NE27208 2.452 1.582 1.615 MET922 SD7245 2.131 1.439 1.748 1.108 HIS931 NE27320 2.014 0.695 0.704 1.130 1.106 HIS936 NE27361 3.612 2.415 2.199 1.312 1.982 1.758 HIS940 NE27398 3.969 2.725 2.424 1.728 2.459 2.092 0.501 CYS971 SG7630 1.026 1.229 1.407 2.263 2.378 1.823 3.283 MET983 SD7740 1.738 0.970 1.084 2.500 2.163 1.428 3.104 CYS984 SG7747 1.937 0.790 0.528 2.128 2.106 1.110 2.630 HIS994 NE27836 3.472 2.296 2.070 3.194 2.934 2.170 3.046 MET1004 SD7916 4.483 3.136 2.882 3.162 3.062 2.619 2.380 MET1005 SD7924 4.155 2.821 2.611 2.564 2.513 2.212 1.744 MET1010 SD7954 3.936 2.627 2.426 2.039 2.173 1.952 1.105 MET1040 SD8205 2.685 1.774 1.361 2.871 3.096 2.021 3.142 MET1043 SD8231 2.171 0.979 0.453 1.855 2.160 1.084 2.282 HIS1047 NE28263 1.945 0.915 0.524 1.788 2.137 1.144 2.387 HIS1048 NE28273 2.488 1.833 1.535 1.986 2.735 1.935 2.551 MET1055 SD8325 2.644 1.858 1.598 3.206 3.182 2.193 3.529 HIS940 CYS971 MET983 CYS984 HIS994 MET1004 MET1005 NE27398 SG7630 SD7740 SG7747 NE27836 SD7916 SD7924 CYS971 SG7630 3.537 MET983 SD7740 3.355 1.644 CYS984 SG7747 2.823 1.496 0.694 HIS994 NE27836 3.136 3.261 1.783 1.782 MET1004 SD7916 2.370 4.279 3.115 2.910 1.759 MET1005 SD7924 1.813 3.983 3.014 2.762 2.059 0.728 MET1010 SD7954 1.234 3.733 3.032 2.698 2.440 1.368 0.668 MET1040 SD8205 3.179 1.945 1.521 1.055 2.046 3.269 3.268 MET1043 SD8231 2.418 1.505 1.310 0.625 2.103 2.942 2.726 HIS1047 NE28263 2.548 1.204 1.390 0.775 2.415 3.248 2.990 HIS1048 NE28273 2.614 1.565 2.437 1.840 3.367 3.948 3.620 MET1055 SD8325 3.619 2.132 1.214 1.107 1.747 3.277 3.362 MET1010 MET1040 MET1043 HIS1047 HIS1048 SD7954 SD8205 SD8231 NE28263 NE28273 MET1040 SD8205 3.251 MET1043 SD8231 2.551 1.017 HIS1047 NE28263 2.765 1.171 0.343 HIS1048 NE28273 3.258 1.818 1.297 1.071 MET1055 SD8325 3.455 0.730 1.433 1.597 2.439 Start terminus MET-16: NH3+ End terminus ASN-157: COO- Checking for duplicate atoms.... Now there are 1021 residues with 10670 atoms Making bonds... Warning: Long Bond (3044-3046 = 2.82265 nm) Warning: Long Bond (4010-4012 = 0.607314 nm) Warning: Long Bond (4995-4997 = 0.612655 nm) Warning: Long Bond (9491-9493 = 0.796238 nm) Number of bonds was 10864, now 10859 Generating angles, dihedrals and pairs... Before cleaning: 17427 pairs ------------------------------------------------------- Program pdb2gmx, VERSION 4.5.5 Source code file: pgutil.c, line: 91 Fatal error: Atom N is used in an interaction of type improper in the topology database, but an atom of that name was not found in residue number 3. second: gmx pdb2gmx -f *.pdb -o *.gro -p topol.top -ignh -water spc -missing so in this step, the mentioned error was solved. however after applying the next commands such as *gmx grompp -f ions.mdp -c *.pdb -p topol.top -o ions.tpr* *another error was occurred:*Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file topol.top, line 42200]: No default G96Angle types ERROR 2 [file topol.top, line 42201]: No default G96Angle types ERROR 3 [file topol.top, line 42202]: No default G96Angle types ERROR 4 [file topol.top, line 51715]: No default G96Angle types ERROR 5 [file topol.top, line 51716]: No default G96Angle types ERROR 6 [file topol.top, line 51717]: No default G96Angle types ERROR 7 [file topol.top, line 56644]: No default Proper Dih. types ERROR 8 [file topol.top, line 61568]: No default Proper Dih. types Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 66972]: System has non-zero total charge: -13.645993 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. There was 1 note There was 1 warning ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 1372 Fatal error: There were 8 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors *thanks in advances for your attention * *I am looking forward to getting your answer* *best wishes* *Marzieh* -- *Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics (IBB)University of Tehran, Tehran- Iran.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.