# Error in running pdb2gmx for protein with modified residue **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx\ **Created:** [September 28, 2023, 5:47pm UTC](https://gromacs.bioexcel.eu/t/error-in-running-pdb2gmx-for-protein-with-modified-residue/7288 "2023-09-28T17:47:05Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![srikrishnan\_b](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/srikrishnan_b/32/2474_2.png) [@srikrishnan\_b](https://gromacs.bioexcel.eu/u/srikrishnan_b)\ **Post date:** [September 28, 2023, 5:47pm UTC](https://gromacs.bioexcel.eu/t/error-in-running-pdb2gmx-for-protein-with-modified-residue/7288/1 "2023-09-28T17:47:05Z")
GROMACS version: 2021.4-Ubuntu-2021.4-2 GROMACS modification: No Here post your question I am trying to run pdb2gmx for a pdb with a modified residue with Amber96 forcefield and TIP3P water. I have modified aminoacids.rtp and aminoacids.hdb files to include the modified residue (chromophore in 1bfp). When I am running, the following error comes: > Fatal error: > Residue 66 named IIC of a molecule in the input file was mapped > to an entry in the topology database, but the atom C used in > that entry is not found in the input file. Perhaps your atom > and/or residue naming needs to be fixed. But the rtp does not have C, and the entries in the rtp file and the input pdb are matching. Here is the rtp entry for the modified residue: [IIC] [atoms] N1 N -0.548582 1 H H 0.400399 2 CA1 CT -0.101469 3 HA1 H1 0.214310 4 CB1 CT -0.068149 5 HB11 H1 0.260349 6 HB12 H1 0.171718 7 OG1 OH -0.642600 8 HG1 H1 0.424967 9 CA3 CT -0.290798 10 HA31 H1 0.208999 11 HA32 H1 0.152438 12 C3 C 0.573572 13 O3 O -0.542998 14 C1 CK 0.598230 15 N2 NB -0.672233 16 CA2 CC 0.220947 17 C2 CC 0.565509 18 O2 O -0.494683 19 N3 N\* -0.510388 20 CB2 CM 0.224631 21 HB2 HC 0.183086 22 CG2 CC 0.324378 23 ND1 NB -0.619765 24 CE1 CR 0.223150 25 HE1 H5 0.164588 26 NE2 NA -0.421035 27 HE2 H 0.347920 28 CD2 CW -0.051955 29 HD2 H4 0.154726 30 Here is the residue IIC in the input file: ATOM 481 C1 IIC A 65 26.589 27.058 37.112 1.00 5.23 C ATOM 482 N2 IIC A 65 27.875 27.700 37.197 1.00 8.50 N ATOM 483 CA2 IIC A 65 28.092 28.054 38.561 1.00 9.52 C ATOM 484 C2 IIC A 65 26.899 27.674 39.362 1.00 1.00 C ATOM 485 O2 IIC A 65 26.769 27.659 40.557 1.00 22.50 O ATOM 486 N3 IIC A 65 26.065 27.009 38.390 1.00 16.14 N ATOM 487 CA1 IIC A 65 25.925 26.647 35.850 1.00 3.62 C ATOM 488 N1 IIC A 65 24.947 27.619 35.442 1.00 30.34 N ATOM 489 CB1 IIC A 65 26.790 26.236 34.651 1.00 19.32 C ATOM 490 OG1 IIC A 65 27.734 25.285 35.063 1.00 18.74 O ATOM 491 CA3 IIC A 65 24.719 26.554 38.680 1.00 17.05 C ATOM 492 C3 IIC A 65 24.595 25.182 39.315 1.00 6.60 C ATOM 493 O3 IIC A 65 23.733 24.940 40.139 1.00 23.88 O ATOM 494 CB2 IIC A 65 29.212 28.660 39.007 1.00 19.99 C ATOM 495 CG2 IIC A 65 30.330 29.074 38.098 1.00 9.87 C ATOM 496 ND1 IIC A 65 30.322 28.828 36.727 1.00 12.20 N ATOM 497 CE1 IIC A 65 31.407 29.416 36.217 1.00 20.41 C ATOM 498 NE2 IIC A 65 32.150 29.936 37.202 1.00 13.18 N ATOM 499 CD2 IIC A 65 31.494 29.748 38.398 1.00 15.02 C From the terminal: ``` gmx pdb2gmx -f 1bfpclean.pdb -o bfppro.gro :-) GROMACS - gmx pdb2gmx, 2021.4-Ubuntu-2021.4-2 (-: 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](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 2021.4-Ubuntu-2021.4-2 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /mnt/f/BioSim/Project Command line: gmx pdb2gmx -f 1bfpclean.pdb -o bfppro.gro Select the Force Field: From current directory: 1: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) From ‘/usr/share/gromacs/top’: 2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 10: GROMOS96 43a1 force field 11: GROMOS96 43a2 force field (improved alkane dihedrals) 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 15: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 10.1002/jcc.21675) 16: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9) 17: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 1 Using the Amber96 force field in directory ./amber96.ff Opening force field file ./amber96.ff/watermodels.dat Select the Water Model: 1: TIP3P TIP 3-point, recommended 2: TIP4P TIP 4-point 3: TIP4P-Ew TIP 4-point optimized with Ewald 4: TIP5P TIP 5-point 5: SPC simple point charge 6: SPC/E extended simple point charge 7: None 1 going to rename ./amber96.ff/aminoacids.r2b Opening force field file ./amber96.ff/aminoacids.r2b going to rename ./amber96.ff/dna.r2b Opening force field file ./amber96.ff/dna.r2b going to rename ./amber96.ff/rna.r2b Opening force field file ./amber96.ff/rna.r2b Reading 1bfpclean.pdb… WARNING: all CONECT records are ignored Read ‘BLUE FLUORESCENT PROTEIN’, 1818 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 227 residues with 1818 atoms chain #res #atoms 1 ‘A’ 227 1818 there were 8 atoms with zero occupancy and 0 atoms with occupancy unequal to one (out of 1818 atoms). Check your pdb file. there were 8 atoms with zero occupancy and 0 atoms with occupancy unequal to one (out of 1818 atoms). Check your pdb file. Opening force field file ./amber96.ff/atomtypes.atp Reading residue database… (Amber96) Opening force field file ./amber96.ff/aminoacids.rtp Opening force field file ./amber96.ff/dna.rtp Opening force field file ./amber96.ff/rna.rtp Opening force field file ./amber96.ff/aminoacids.hdb Opening force field file ./amber96.ff/dna.hdb Opening force field file ./amber96.ff/rna.hdb Opening force field file ./amber96.ff/aminoacids.n.tdb Opening force field file ./amber96.ff/aminoacids.c.tdb Processing chain 1 ‘A’ (1818 atoms, 227 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 340 donors and 343 acceptors were found. There are 557 hydrogen bonds Will use HISE for residue 25 Will use HISE for residue 75 Will use HISE for residue 79 Will use HISE for residue 137 Will use HISD for residue 146 Will use HISE for residue 167 Will use HISE for residue 179 Will use HISH for residue 197 Will use HISD for residue 215 Identified residue MET1 as a starting terminus. Identified residue ILE227 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: MET1 HIS25 CYS48 CYS68 HIS75 MET76 HIS79 SD7 NE2185 SG356 SG521 NE2586 SD593 NE2624 HIS25 NE2185 5.125 CYS48 SG356 4.404 1.196 CYS68 SG521 1.988 3.235 2.420 HIS75 NE2586 1.633 4.635 4.033 2.011 MET76 SD593 1.629 4.250 3.668 1.672 0.410 HIS79 NE2624 1.270 4.491 3.971 1.829 0.827 0.685 MET86 SD681 1.876 3.426 2.636 0.519 2.286 1.962 1.950 HIS137 NE21099 4.852 0.832 1.050 2.957 4.165 3.809 4.158 HIS146 NE21180 2.986 2.731 2.326 1.630 1.988 1.647 2.069 MET151 SD1222 2.505 3.527 3.356 2.013 1.879 1.550 1.411 HIS167 NE21356 3.786 1.903 1.779 2.162 2.901 2.550 2.905 HIS179 NE21446 3.281 2.129 1.900 1.712 2.557 2.173 2.431 HIS197 NE21585 1.710 3.772 3.258 1.314 1.040 0.642 0.737 HIS215 NE21731 4.296 2.178 1.200 2.413 3.704 3.414 3.885 MET216 SD1738 3.724 1.954 1.181 1.850 3.041 2.712 3.145 MET86 HIS137 HIS146 MET151 HIS167 HIS179 HIS197 SD681 NE21099 NE21180 SD1222 NE21356 NE21446 NE21585 HIS137 NE21099 3.260 HIS146 NE21180 2.075 2.216 MET151 SD1222 2.173 3.304 1.526 HIS167 NE21356 2.545 1.382 0.916 2.041 HIS179 NE21446 2.048 1.780 0.739 1.551 0.605 HIS197 NE21585 1.562 3.422 1.368 1.059 2.187 1.712 HIS215 NE21731 2.779 1.577 2.195 3.574 1.917 2.157 3.200 MET216 SD1738 2.259 1.342 1.340 2.691 1.080 1.262 2.427 HIS215 NE21731 MET216 SD1738 0.902 Opening force field file ./amber96.ff/aminoacids.arn Opening force field file ./amber96.ff/dna.arn Opening force field file ./amber96.ff/rna.arn Checking for duplicate atoms… Generating any missing hydrogen atoms and/or adding termini. * * * Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2 Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 191) Fatal error: Residue 66 named IIC of a molecule in the input file was mapped to an entry in the topology database, but the atom C used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. How do I resolve this error? ---
**Author:** ![Neena](https://avatars.discourse-cdn.com/v4/letter/n/bc79bd/32.png) [@Neena](https://gromacs.bioexcel.eu/u/Neena)\ **Post date:** [September 30, 2023, 2:04am UTC](https://gromacs.bioexcel.eu/t/error-in-running-pdb2gmx-for-protein-with-modified-residue/7288/2 "2023-09-30T02:04:09Z")
> [@srikrishnan\_b](#): > > Fatal error: > Residue 66 named IIC of a molecule in the input file was mapped > to an entry in the topology database, but the atom C used in > that entry is not found in the input file. Perhaps your atom > and/or residue naming needs to be fixed. There might be some discrepancy in atom naming of modified residue IIC in the input PDB file vs files in the topology database. > [@srikrishnan\_b](#): > > I have modified aminoacids.rtp and aminoacids.hdb files to include the modified residue In the aminoacids.rtp file, did you check if the improper dihedrals are also modified? When I added a modified residue as the C-terminal residue, I had to edit the following files in addition to the ones you mentioned: atomtypes.atp, ffnonbonded.itp, ffbonded.itp, residuetypes.dat (this file both in forcefield and working directory)