gmx pdb2gmx -f final_drug_bound_1.pdb -o nter_cter_3g5d_processed.gro -ff oplsaa -water tip4p -ter :-) GROMACS - gmx pdb2gmx, 2021.5 (-: GROMACS is written by: Andrey Alekseenko Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Gilles Gouaillardet Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx pdb2gmx, version 2021.5 Executable: /usr/local/bin/gmx Data prefix: /usr/local Working dir: /home/iiit/work/ccnsb/Kinase/modelling/kinase_paper_modelling Command line: gmx pdb2gmx -f final_drug_bound_1.pdb -o nter_cter_3g5d_processed.gro -ff oplsaa -water tip4p -ter Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Opening force field file /usr/local/share/gromacs/top/oplsaa.ff/aminoacids.r2b Reading final_drug_bound_1.pdb... Read 'MDANALYSIS FRAME 0: Created by PDBWriter', 4974 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 2 chains and 1 blocks of water and 401 residues with 4974 atoms chain #res #atoms 1 'A' 286 4573 2 'H' 1 59 3 ' ' 114 342 (only water) All occupancies are one All occupancies are one Opening force field file /usr/local/share/gromacs/top/oplsaa.ff/atomtypes.atp Opening force field file /usr/local/share/gromacs/top/oplsaa.ff/dasatinib.atp Reading residue database... (Oplsaa) Opening force field file /usr/local/share/gromacs/top/oplsaa.ff/aminoacids.rtp Opening force field file /usr/local/share/gromacs/top/oplsaa.ff/dasatinib.rtp Reading .rtp file without '[ bondedtypes ]' directive, Will proceed as if the entry was: Reading .rtp file without '[ bondedtypes ]' directive, Will proceed as if the entry was: [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih 1 1 1 2 0 3 1 1 Opening force field file /usr/local/share/gromacs/top/oplsaa.ff/aminoacids.hdb Opening force field file /usr/local/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb Opening force field file /usr/local/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.23# Processing chain 1 'A' (4573 atoms, 286 residues) Identified residue GLY248 as a starting terminus. Identified residue LEU533 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HISD249 MET250 CYS277 MET283 MET302 MET314 HISD319 NE222 SD37 SG466 SD562 SD854 SD1035 NE21141 MET250 SD37 0.869 CYS277 SG466 3.160 2.643 MET283 SD562 4.503 4.120 2.127 MET302 SD854 2.312 1.579 1.459 3.364 MET314 SD1035 3.056 2.856 1.323 1.791 2.359 HISD319 NE21141 4.023 4.089 2.738 2.479 3.811 1.541 MET341 SD1507 4.197 3.994 2.078 1.143 3.384 1.190 1.356 CYS345 SG1561 4.556 4.203 1.707 1.520 3.164 1.641 2.130 MET354 SD1708 5.709 5.420 3.045 1.780 4.497 2.658 2.484 MET366 SD1915 5.186 5.001 2.771 2.063 4.187 2.183 1.707 MET374 SD2016 3.855 3.802 2.111 2.515 3.231 1.317 1.021 MET380 SD2119 3.199 3.390 2.632 2.970 3.373 1.474 0.962 HISD384 NE22189 3.610 3.446 1.551 2.188 2.739 0.938 1.369 CYS400 SG2439 4.765 4.596 2.469 1.817 3.856 1.757 1.352 MET466 SD3489 5.532 5.259 3.056 3.873 4.091 3.335 3.409 MET481 SD3746 5.336 5.117 2.868 3.353 4.066 2.861 2.718 CYS483 SG3774 6.128 5.998 3.801 3.797 5.071 3.501 2.864 CYS487 SG3828 5.836 5.707 3.507 3.390 4.817 3.124 2.466 HISD492 NE23903 5.735 5.615 3.515 3.825 4.697 3.286 2.769 MET495 SD3949 5.432 5.306 3.174 3.353 4.418 2.851 2.321 CYS496 SG3963 5.576 5.504 3.544 3.961 4.662 3.258 2.683 CYS498 SG3991 4.819 4.791 2.975 3.354 4.098 2.458 1.803 MET341 CYS345 MET354 MET366 MET374 MET380 HISD384 SD1507 SG1561 SD1708 SD1915 SD2016 SD2119 NE22189 CYS345 SG1561 1.215 MET354 SD1708 1.607 1.398 MET366 SD1915 1.314 1.210 0.971 MET374 SD2016 1.490 1.614 2.426 1.569 MET380 SD2119 1.966 2.628 3.315 2.530 1.243 HISD384 NE22189 1.338 1.292 2.374 1.673 0.564 1.484 CYS400 SG2439 0.914 1.083 1.201 0.449 1.262 2.146 1.333 MET466 SD3489 3.325 2.354 3.059 2.555 2.497 3.674 2.472 MET481 SD3746 2.688 1.858 2.426 1.812 1.901 3.113 1.967 CYS483 SG3774 3.034 2.483 2.440 1.833 2.372 3.456 2.634 CYS487 SG3828 2.602 2.132 2.069 1.398 2.027 3.111 2.293 HISD492 NE23903 3.021 2.420 2.693 1.981 2.119 3.215 2.369 MET495 SD3949 2.524 1.995 2.270 1.498 1.706 2.835 1.960 CYS496 SG3963 3.087 2.575 2.928 2.137 2.030 3.050 2.331 CYS498 SG3991 2.365 2.120 2.620 1.689 1.165 2.146 1.568 CYS400 MET466 MET481 CYS483 CYS487 HISD492 MET495 SG2439 SD3489 SD3746 SG3774 SG3828 NE23903 SD3949 MET466 SD3489 2.694 MET481 SD3746 1.970 0.790 CYS483 SG3774 2.142 1.685 1.120 CYS487 SG3828 1.703 1.801 1.092 0.447 HISD492 NE23903 2.193 1.294 0.776 0.582 0.753 MET495 SD3949 1.692 1.464 0.726 0.696 0.518 0.503 CYS496 SG3963 2.294 1.436 0.976 0.870 0.992 0.368 0.660 CYS498 SG3991 1.685 1.876 1.239 1.412 1.203 1.084 0.808 CYS496 SG3963 CYS498 SG3991 0.911 Select start terminus type for GLY-248 0: GLY-NH3+ 1: GLY-ZWITTERION_NH3+ (only use with zwitterions containing exactly one residue) 2: GLY-NH2 3: None 0 Start terminus GLY-248: GLY-NH3+ Select end terminus type for LEU-533 0: COO- 1: ZWITTERION_COO- (only use with zwitterions containing exactly one residue) 2: COOH 3: None 0 End terminus LEU-533: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 286 residues with 4574 atoms Chain time... Back Off! I just backed up topol_Protein_chain_A.itp to ./#topol_Protein_chain_A.itp.14# Making bonds... Number of bonds was 4629, now 4629 Generating angles, dihedrals and pairs... Before cleaning: 12150 pairs Before cleaning: 12285 dihedrals Keeping all generated dihedrals Making cmap torsions... There are 12285 dihedrals, 915 impropers, 8380 angles 12063 pairs, 4629 bonds and 0 virtual sites Total mass 32700.840 a.m.u. Total charge -5.000 e Writing topology Back Off! I just backed up posre_Protein_chain_A.itp to ./#posre_Protein_chain_A.itp.12# Processing chain 2 'H' (59 atoms, 1 residues) No residues in chain starting at 1N11 identified as Protein/RNA/DNA. This makes it impossible to link them into a molecule, which could either be correct or a catastrophic error. Please check your structure, and add all necessary residue names to residuetypes.dat if this was not correct. No residues in chain starting at 1N11 identified as Protein/RNA/DNA. This makes it impossible to link them into a molecule, which could either be correct or a catastrophic error. Please check your structure, and add all necessary residue names to residuetypes.dat if this was not correct. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 1 residues with 59 atoms Chain time... Back Off! I just backed up topol_Other_chain_H.itp to ./#topol_Other_chain_H.itp.5# Making bonds... Number of bonds was 62, now 62 Generating angles, dihedrals and pairs... Before cleaning: 143 pairs Before cleaning: 148 dihedrals Making cmap torsions... There are 148 dihedrals, 17 impropers, 107 angles 134 pairs, 62 bonds and 0 virtual sites Total mass 488.009 a.m.u. Total charge 0.000 e Writing topology Back Off! I just backed up posre_Other_chain_H.itp to ./#posre_Other_chain_H.itp.4# Processing chain 3 (342 atoms, 114 residues) Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully ------------------------------------------------------- Program: gmx pdb2gmx, version 2021.5 Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 790) Fatal error: Atom OH2 in residue HO4 3 was not found in rtp entry HO4 with 4 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -------------------------------------------------------