# Pdb2gmx broken for single-residue structures in GROMACS 2021.1 **URL:** https://gromacs.bioexcel.eu/t/pdb2gmx-broken-for-single-residue-structures-in-gromacs-2021-1/1973 **Category:** User discussions **Tags:** pdb2gmx **Created:** [April 16, 2021, 12:06pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-broken-for-single-residue-structures-in-gromacs-2021-1/1973 "2021-04-16T12:06:37Z") **Posts on this page:** 8 **Page:** 1
### Author: ![jakubecd](https://avatars.discourse-cdn.com/v4/letter/j/7993a0/32.png) [@jakubecd](https://gromacs.bioexcel.eu/u/jakubecd) #### Post date: [April 16, 2021, 12:06pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-broken-for-single-residue-structures-in-gromacs-2021-1/1973/1 "2021-04-16T12:06:37Z")
GROMACS version: 2021.1 GROMACS modification: No I have prepared a single-residue structure (`GLU.pdb`) using PyMOL: ``` HEADER GLU ATOM 1 N GLU X 1 -0.517 -2.346 -1.038 1.00 0.00 N ATOM 2 CA GLU X 1 0.042 -0.997 -1.038 1.00 0.00 C ATOM 3 C GLU X 1 1.551 -1.037 -1.038 1.00 0.00 C ATOM 4 O GLU X 1 2.180 -2.105 -1.038 1.00 0.00 O ATOM 5 CB GLU X 1 -0.481 -0.212 0.199 1.00 0.00 C ATOM 6 CG GLU X 1 -0.006 1.273 0.310 1.00 0.00 C ATOM 7 CD GLU X 1 -0.430 2.077 1.525 1.00 0.00 C ATOM 8 OE1 GLU X 1 -1.158 1.575 2.403 1.00 0.00 O ATOM 9 OE2 GLU X 1 -0.000 3.247 1.597 1.00 0.00 O1- ATOM 10 H GLU X 1 0.110 -3.225 -1.038 1.00 0.00 H ATOM 11 HA GLU X 1 -0.284 -0.479 -1.958 1.00 0.00 H ATOM 12 2HB GLU X 1 -0.192 -0.743 1.129 1.00 0.00 H ATOM 13 3HB GLU X 1 -1.588 -0.222 0.212 1.00 0.00 H ATOM 14 2HG GLU X 1 -0.316 1.858 -0.571 1.00 0.00 H ATOM 15 3HG GLU X 1 1.094 1.340 0.339 1.00 0.00 H END ``` In GROMACS 2020.3, topology can be prepared for it successfully using `gmx pdb2gmx -f GLU.pdb -ff charmm36-jul2020 -ter -ignh`: ``` Command line: gmx pdb2gmx -f GLU.pdb -ff charmm36-jul2020 -ter -ignh Using the Charmm36-jul2020 force field in directory charmm36-jul2020.ff Opening force field file /home/david/Programs/gromacs-2020.3/share/gromacs/top/charmm36-jul2020.ff/watermodels.dat Select the Water Model: 1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H 2: TIP4P TIP 4-point 3: TIP5P TIP 5-point 4: SPC simple point charge 5: SPC/E extended simple point charge 6: None 1 going to rename charmm36-jul2020.ff/merged.r2b Opening force field file /home/david/Programs/gromacs-2020.3/share/gromacs/top/charmm36-jul2020.ff/merged.r2b Reading GLU.pdb... Read 'GLU', 9 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 1 residues with 9 atoms chain #res #atoms 1 'X' 1 9 All occupancies are one Opening force field file /home/david/Programs/gromacs-2020.3/share/gromacs/top/charmm36-jul2020.ff/atomtypes.atp Reading residue database... (Charmm36-jul2020) Opening force field file /home/david/Programs/gromacs-2020.3/share/gromacs/top/charmm36-jul2020.ff/merged.rtp Opening force field file /home/david/Programs/gromacs-2020.3/share/gromacs/top/charmm36-jul2020.ff/merged.hdb Opening force field file /home/david/Programs/gromacs-2020.3/share/gromacs/top/charmm36-jul2020.ff/merged.n.tdb Opening force field file /home/david/Programs/gromacs-2020.3/share/gromacs/top/charmm36-jul2020.ff/merged.c.tdb Back Off! I just backed up topol.top to ./#topol.top.12# Processing chain 1 'X' (9 atoms, 1 residues) Identified residue GLU1 as a starting terminus. Identified residue GLU1 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for GLU-1 0: NH3+ 1: NH2 2: 5TER 3: None 0 Start terminus GLU-1: NH3+ Select end terminus type for GLU-1 0: COO- 1: COOH 2: CT2 3: 3TER 4: None 0 End terminus GLU-1: COO- Opening force field file /home/david/Programs/gromacs-2020.3/share/gromacs/top/charmm36-jul2020.ff/merged.arn Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 1 residues with 18 atoms Making bonds... Number of bonds was 17, now 17 Generating angles, dihedrals and pairs... Before cleaning: 39 pairs Before cleaning: 39 dihedrals Keeping all generated dihedrals Making cmap torsions... There are 39 dihedrals, 2 impropers, 30 angles 39 pairs, 17 bonds and 0 virtual sites Total mass 146.123 a.m.u. Total charge -1.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.5# Writing coordinate file... Back Off! I just backed up conf.gro to ./#conf.gro.5# --------- PLEASE NOTE ------------ You have successfully generated a topology from: GLU.pdb. The Charmm36-jul2020 force field and the tip3p water model are used. --------- ETON ESAELP ------------ ``` However, using GROMACS 2021.1, weird things occur. First, using `gmx pdb2gmx -f GLU.pdb -ff charmm36-feb2021 -ter -ignh`, the following output results: ``` Command line: gmx pdb2gmx -f GLU.pdb -ff charmm36-feb2021 -ter -ignh Using the Charmm36-feb2021 force field in directory charmm36-feb2021.ff Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/watermodels.dat Select the Water Model: 1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H 2: TIP4P TIP 4-point 3: TIP5P TIP 5-point 4: SPC simple point charge 5: SPC/E extended simple point charge 6: None 1 going to rename charmm36-feb2021.ff/merged.r2b Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.r2b Reading GLU.pdb... Read 'GLU', 9 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 1 residues with 9 atoms chain #res #atoms 1 'X' 1 9 All occupancies are one All occupancies are one Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/atomtypes.atp Reading residue database... (Charmm36-feb2021) Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.rtp Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.hdb Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.n.tdb Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.c.tdb Back Off! I just backed up topol.top to ./#topol.top.11# Processing chain 1 'X' (9 atoms, 1 residues) Identified residue GLU1 as a starting terminus. Identified residue GLU1 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.arn Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 1 residues with 15 atoms Making bonds... Number of bonds was 14, now 14 Generating angles, dihedrals and pairs... Before cleaning: 30 pairs Before cleaning: 30 dihedrals Keeping all generated dihedrals Making cmap torsions... There are 30 dihedrals, 2 impropers, 23 angles 30 pairs, 14 bonds and 0 virtual sites Total mass 128.107 a.m.u. Total charge -1.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.4# Writing coordinate file... Back Off! I just backed up conf.gro to ./#conf.gro.4# --------- PLEASE NOTE ------------ You have successfully generated a topology from: GLU.pdb. The Charmm36-feb2021 force field and the tip3p water model are used. --------- ETON ESAELP ------------ ``` Despite the `-ter` switch, I am not prompted for the termini at all. The topology, however, looks like this: ``` [atoms] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 GLU rtp GLU q -1.0 1 NH1 1 GLU N 1 -0.47 14.007 2 H 1 GLU HN 2 0.31 1.008 3 CT1 1 GLU CA 3 0.07 12.011 4 HB1 1 GLU HA 4 0.09 1.008 5 CT2A 1 GLU CB 5 -0.18 12.011 6 HA2 1 GLU HB1 6 0.09 1.008 7 HA2 1 GLU HB2 7 0.09 1.008 8 CT2 1 GLU CG 8 -0.28 12.011 9 HA2 1 GLU HG1 9 0.09 1.008 10 HA2 1 GLU HG2 10 0.09 1.008 11 CC 1 GLU CD 11 0.62 12.011 12 OC 1 GLU OE1 12 -0.76 15.999 13 OC 1 GLU OE2 13 -0.76 15.999 14 C 1 GLU C 14 0.51 12.011 15 O 1 GLU O 15 -0.51 15.999 ; qtot -1 ``` That is, the termini are not charged – the topology corresponds to a glutamate residue which would be a part of a chain. Even more weird, when the water model is specified in the command `gmx pdb2gmx -f GLU.pdb -ff charmm36-feb2021 -water tip3p -ter -ignh`, the following error occurs: ``` Command line: gmx pdb2gmx -f GLU.pdb -ff charmm36-feb2021 -water tip3p -ter -ignh Using the Charmm36-feb2021 force field in directory charmm36-feb2021.ff going to rename charmm36-feb2021.ff/merged.r2b Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.r2b Reading GLU.pdb... Read 'GLU', 9 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 1 residues with 9 atoms chain #res #atoms 1 'X' 1 9 All occupancies are one All occupancies are one Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/atomtypes.atp Reading residue database... (Charmm36-feb2021) Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.rtp Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.hdb Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.n.tdb Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.c.tdb Back Off! I just backed up topol.top to ./#topol.top.10# Processing chain 1 'X' (9 atoms, 1 residues) Identified residue GLU1 as a starting terminus. Identified residue GLU1 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Opening force field file /home/david/Programs/gromacs-2021.1/share/gromacs/top/charmm36-feb2021.ff/merged.arn Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 1 residues with 15 atoms Making bonds... Number of bonds was 14, now 14 Generating angles, dihedrals and pairs... Before cleaning: 30 pairs ------------------------------------------------------- Program: gmx pdb2gmx, version 2021.1 Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 151) Fatal error: Residue 21949 named GLU of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper 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 http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- ``` This is obviously broken. ---
### Author: ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla) #### Post date: [April 20, 2021, 11:04am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-broken-for-single-residue-structures-in-gromacs-2021-1/1973/2 "2021-04-20T11:04:41Z")
Hi, Did you try gmx2021.1 and `charmm36-jul2020` forcefield? The last case it looks to me a bug (wrong error message?). Please report it in GitLab with all the connected inputs. Please check that someone did not already report it. Best regards Alessandra ---
### Author: ![pbauer](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pbauer/32/13_2.png) [@pbauer](https://gromacs.bioexcel.eu/u/pbauer) #### Post date: [April 20, 2021, 11:19am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-broken-for-single-residue-structures-in-gromacs-2021-1/1973/3 "2021-04-20T11:19:24Z")
This looks like an actual bug, will investigate and see that we have an open issue for that. ---
### Author: ![pbauer](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pbauer/32/13_2.png) [@pbauer](https://gromacs.bioexcel.eu/u/pbauer) #### Post date: [April 20, 2021, 2:33pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-broken-for-single-residue-structures-in-gromacs-2021-1/1973/4 "2021-04-20T14:33:55Z")
So, when trying to reproduce this I can confirm that the termini selection doesn’t work, but the water model issue doesn’t happen to me. This might be an issue with the updated charmm forcefield? I opened [pdb2gmx termini selection doesn't work (#4029) · Issues · GROMACS / GROMACS · GitLab](https://gitlab.com/gromacs/gromacs/-/issues/4029) for it. ---
### Author: ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul) #### Post date: [April 20, 2021, 2:45pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-broken-for-single-residue-structures-in-gromacs-2021-1/1973/5 "2021-04-20T14:45:55Z")
> [@pbauer](#): > > This might be an issue with the updated charmm forcefield? I don’t see how. The only change from February to July 2020 was inclusion of NBFIX terms that were missing, and the OP reports that version 2020.3 works with the same version that fails in 2021. ---
### Author: ![pbauer](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pbauer/32/13_2.png) [@pbauer](https://gromacs.bioexcel.eu/u/pbauer) #### Post date: [April 20, 2021, 2:58pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-broken-for-single-residue-structures-in-gromacs-2021-1/1973/6 "2021-04-20T14:58:37Z")
Ok, then there are likely two bugs, as I can’t reproduce the one coming from selecting the water model locally when using the charmm36-jul2020 forcefield. Will see that I update the GitLab issue. Thanks @jalemkul for checking1 ---
### Author: ![jakubecd](https://avatars.discourse-cdn.com/v4/letter/j/7993a0/32.png) [@jakubecd](https://gromacs.bioexcel.eu/u/jakubecd) #### Post date: [April 21, 2021, 9:26am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-broken-for-single-residue-structures-in-gromacs-2021-1/1973/7 "2021-04-21T09:26:23Z")
Hello, thank you all for your responses. I have done some additional testing on these issues. The “water issue” I described above actually occurs with `charmm36-feb2021` only when **both** the force field and water model are selected from the command line simultaneously (so the command is `gmx pdb2gmx -f GLU.pdb -ff charmm36-feb2021 -water tip3p -ter -ignh`). When only the FF or the water model (or neither) are selected from the command line (_i.e._, when interactive selection is needed), `pdb2gmx` finishes “successfully” (though the termini are still not added as described). However, when I use the “Charmm27” FF included with GROMACS, the situation is exactly the opposite: both the FF and water model **need** to be selected from the command line (`gmx pdb2gmx -f GLU.pdb -ff charmm27 -water tip3p -ter -ignh`), otherwise the same kind of error occurs: ``` Fatal error: Residue 22066 named GLU of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. ``` Please note that the “residue number” in the error message is different; this generally changes depending on whether the FF or the water model are selected from the command line. Both of the described issues (termini selection left out/command line options) disappear when the chains contain more than 1 residue, regardless of the FF and water model used and regardless of whether they are selected interactively or using a command line option (tested with an alanine pentapeptide prepared in PyMOL). I’ll just add that I’ve built and use GROMACS on Ubuntu 20.04 with CUDA support, and the build completed and was tested with `make check` without errors. If I were to guess, could maybe some bugs have been introduced with the new “cyclic molecule” support in `pdb2gmx`? David ---
### Author: ![pbauer](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pbauer/32/13_2.png) [@pbauer](https://gromacs.bioexcel.eu/u/pbauer) #### Post date: [April 21, 2021, 12:50pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-broken-for-single-residue-structures-in-gromacs-2021-1/1973/8 "2021-04-21T12:50:38Z")
Found the bug, fix is here: [Fix incorrect handling of single residue chains (!1467) · Merge requests · GROMACS / GROMACS · GitLab](https://gitlab.com/gromacs/gromacs/-/merge_requests/1467)