# Pdb2gmx Error - molecule in input file was mapped to entry in topology, but atom not found **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx\ **Created:** [June 6, 2023, 1:00pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-error-molecule-in-input-file-was-mapped-to-entry-in-topology-but-atom-not-found/6553 "2023-06-06T13:00:17Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![Zeer](https://avatars.discourse-cdn.com/v4/letter/z/dfb087/32.png) [@Zeer](https://gromacs.bioexcel.eu/u/Zeer)\ **Post date:** [June 6, 2023, 1:00pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-error-molecule-in-input-file-was-mapped-to-entry-in-topology-but-atom-not-found/6553/1 "2023-06-06T13:00:17Z")
GROMACS version: GROMACS modification: Yes/ **No** Here post your question gmx 2020.6-Debian-2020.6-2 - not modified Hello Gromacs Developers and Users, I have been trying to setup a system for my protein structure (Rhodopsin with the retinal chromophore) via the module ‘pdb2gmx’ and have been receiving the following error (output from pdb2gmx): Command line: gmx pdb2gmx -f LYS+RET.pdb -o neo.gro -p a-ARM\_Rh\_GLH-181\_CASTp\_18273.top -ff amber94 -water tip3p Force field ‘amber94’ occurs in 2 places. pdb2gmx is using the one in the current directory. Use interactive selection (not the -ff option) if you would prefer a different one. Using the Amber94 force field in directory ./amber94.ff going to rename ./amber94.ff/aminoacids.r2b Opening force field file ./amber94.ff/aminoacids.r2b going to rename ./amber94.ff/dna.r2b Opening force field file ./amber94.ff/dna.r2b going to rename ./amber94.ff/rna.r2b Opening force field file ./amber94.ff/rna.r2b Reading LYS+RET.pdb… Read ‘’, 3788 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 1 blocks of water and 251 residues with 3788 atoms chain #res #atoms 1 ’ ’ 238 3749 2 ’ ’ 13 39 (only water) All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./amber94.ff/atomtypes.atp Reading residue database… (Amber94) Opening force field file ./amber94.ff/aminoacids.rtp Opening force field file ./amber94.ff/dna.rtp Opening force field file ./amber94.ff/rna.rtp Opening force field file ./amber94.ff/aminoacids.hdb Opening force field file ./amber94.ff/dna.hdb Opening force field file ./amber94.ff/rna.hdb Opening force field file ./amber94.ff/aminoacids.n.tdb Opening force field file ./amber94.ff/aminoacids.c.tdb Back Off! I just backed up a-ARM\_Rh\_GLH-181\_CASTp\_18273.top to ./#a-ARM\_Rh\_GLH-181\_CASTp\_18273.top.1# Processing chain 1 (3749 atoms, 238 residues) Identified residue LYS1 as a starting terminus. Warning: Residue CL246 in chain has different type (‘Ion’) from residue LYS1 (‘Protein’). This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add CL to residuetypes.dat if this was not correct. Warning: Residue CL247 in chain has different type (‘Ion’) from residue LYS1 (‘Protein’). This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add CL to residuetypes.dat if this was not correct. Warning: Residue CL248 in chain has different type (‘Ion’) from residue LYS1 (‘Protein’). This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add CL to residuetypes.dat if this was not correct. Warning: Residue CL249 in chain has different type (‘Ion’) from residue LYS1 (‘Protein’). This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add CL to residuetypes.dat if this was not correct. Warning: Residue CL250 in chain has different type (‘Ion’) from residue LYS1 (‘Protein’). This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add CL to residuetypes.dat if this was not correct. Disabling further warnings about unidentified residues at end of chain. Identified residue VAL232 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS24 MET41 MET46 MET47 CYS49 MET138 CYS139 SG372 SD636 SD722 SD739 SG767 SD2163 SG2177 MET41 SD636 2.067 MET46 SD722 0.891 1.420 MET47 SD739 1.323 1.573 0.627 CYS49 SG767 1.042 1.408 0.890 1.017 MET138 SD2163 3.410 2.740 3.200 2.972 2.424 CYS139 SG2177 4.010 3.087 3.675 3.370 2.993 0.765 CYS144 SG2257 2.913 1.787 2.450 2.196 1.875 1.123 1.319 MET151 SD2368 2.870 1.189 2.266 2.128 1.905 1.883 2.029 CYS172 SG2715 2.158 0.847 1.818 2.027 1.390 2.320 2.786 CYS210 SG3345 1.996 1.939 2.103 2.241 1.258 1.828 2.539 MET216 SD3440 1.006 1.228 0.928 1.340 0.598 2.764 3.343 CYS144 MET151 CYS172 CYS210 SG2257 SD2368 SG2715 SG3345 MET151 SD2368 0.839 CYS172 SG2715 1.638 1.232 CYS210 SG3345 1.779 1.988 1.298 MET216 SD3440 2.176 2.011 1.153 1.315 Opening force field file ./amber94.ff/aminoacids.arn Opening force field file ./amber94.ff/dna.arn Opening force field file ./amber94.ff/rna.arn Checking for duplicate atoms… Generating any missing hydrogen atoms and/or adding termini. * * * Program: gmx pdb2gmx, version 2020.6-Debian-2020.6-2 Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 130) Fatal error: Residue 212 named RET of a molecule in the input file was mapped to an entry in the topology database, but the atom CM used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. ## For more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors) I had generated my .pdb structure from converting a Tinker-xyz file into pdb using a python script ([GitHub - emleddin/pdbxyz-xyzpdb: Scripts to convert between PDB to Tinker XYZ files, without using the existing TINKER programs for conversion.](https://github.com/emleddin/pdbxyz-xyzpdb)). Unfortunately, the residue IDs get a little messed up so I wrote a script to re-ordered the residue ID, as well as change all the atomic names to fit those in Amber94. Additionally, my ligand (chromophore) includes the Retinal chromophore along with the neighboring LYS residue. I am using a topology file that I had previously worked on with another rhodopsin structure which I was able to perform MD with (aminacids.top/.itp/.rtp within the amber94.ff/ directory has been modified to include the Retinal and Lysine as ‘RET’ and used on a previous structure which gave no errors/structural deformity). The current structure Im working on is a mutant of the previous rhodopsin, but differs by AA sequence/Retinal (cis/trans) isomer. So I figured that the same topology files should work for both structures. Could anyone please explain what could be the issue here? And please let me know if additional files are required (e.g. the modified topology/etc. files).