# Pdb2gmx long bond warning **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx\ **Created:** [March 21, 2024, 9:34am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-long-bond-warning/8664 "2024-03-21T09:34:29Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![lcole3](https://avatars.discourse-cdn.com/v4/letter/l/3be4f8/32.png) [@lcole3](https://gromacs.bioexcel.eu/u/lcole3)\ **Post date:** [March 21, 2024, 9:34am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-long-bond-warning/8664/1 "2024-03-21T09:34:29Z")
GROMACS version:2016.3 GROMACS modification: Yes/No I’ve been trying to get topology files for a molecule I’m working on (furfual) using gmx pdb2gmx. However, I get a long bond warning when running this command. When I view the output gro file, I see that none of the atoms are connected; they’re just floating about. The input pdb file is correct, confirmed this visually. Below is my starting pdb configuration. COMPND Furfural AUTHOR GENERATED BY OPEN BABEL 2.3.90 HETATM 1 C1 FUR 1 -5.383 0.620 -0.000 1.00 0.00 C HETATM 2 C2 FUR 1 -5.141 -0.739 -0.000 1.00 0.00 C HETATM 3 C3 FUR 1 -3.772 -0.884 -0.000 1.00 0.00 C HETATM 4 C4 FUR 1 -3.262 0.397 -0.000 1.00 0.00 C HETATM 5 O1 FUR 1 -4.242 1.273 -0.000 1.00 0.00 O HETATM 6 H1 FUR 1 -6.357 1.091 -0.000 1.00 0.00 H HETATM 7 H2 FUR 1 -5.878 -1.531 -0.000 1.00 0.00 H HETATM 8 H3 FUR 1 -3.216 -1.812 -0.000 1.00 0.00 H HETATM 9 C5 FUR 1 -1.838 0.749 -0.000 1.00 0.00 C HETATM 10 O2 FUR 1 -1.493 1.919 -0.000 1.00 0.00 O HETATM 11 H4 FUR 1 -1.084 -0.032 -0.000 1.00 0.00 H MASTER 0 0 0 0 0 0 0 0 11 0 11 0 END Now, I used libpargen and TPPmktop to get an idea of the parameters I need for itp file. I then built the itp and consequently the rtp file from this. I put the rtp and itp files in my forcefield folder (oplsaa), so I can run pdb2gmx.db. Gromacs manual explains adding residues for parameterising molecules with no existing residues in the database, but I figured just adding the rtp/itp files to my working ff directory does the same thing—at least it has before and has worked. This would be my first question: Is having a hand-built rtp file the same as adding residues to the residues.dat? Here are the rtp and itp files I’m using: ;furfural.itp file ; [atomtypes] opls\_140 H4 1.0080 0.000 A 2.50000E-01 1.25520E-01 opls\_567 C4 12.0110 0.000 A 3.55000E-01 2.92880E-01 opls\_570 H3 1.0080 0.000 A 2.42000E-01 1.25520E-01 opls\_566 O1 15.9990 0.000 A 2.90000E-01 5.85760E-01 opls\_141 C5 12.0110 0.000 A 3.55000E-01 2.92880E-01 opls\_568 C3 12.0110 0.000 A 3.55000E-01 2.92880E-01 opls\_570 H2 1.0080 0.000 A 2.42000E-01 1.25520E-01 opls\_278 O2 15.9990 0.000 A 2.96000E-01 8.78640E-01 opls\_567 C1 12.0110 0.000 A 3.55000E-01 2.92880E-01 opls\_569 H1 1.0080 0.000 A 2.42000E-01 1.25520E-01 opls\_568 C2 12.0110 0.000 A 3.55000E-01 2.92880E-01 [moleculetype] ; Name nrexcl FUR 3 [atoms] ; nr type resnr residue atom cgnr charge mass 1 opls\_567 1 FUR C1 1 -0.0710 12.0110 2 opls\_568 1 FUR C2 1 -0.2599 12.0110 3 opls\_568 1 FUR C3 1 -0.1782 12.0110 4 opls\_567 1 FUR C4 1 -0.1566 12.0110 5 opls\_566 1 FUR O1 1 -0.0507 15.9990 6 opls\_569 1 FUR H1 1 0.2330 1.0080 7 opls\_570 1 FUR H2 1 0.1877 1.0080 8 opls\_570 1 FUR H3 1 0.1861 1.0080 9 opls\_141 1 FUR C5 1 0.3431 12.0110 10 opls\_278 1 FUR O2 1 -0.3782 15.9990 11 opls\_140 1 FUR H4 1 0.1447 1.0080 [bonds] 2 1 1 0.1367 456892.800 3 2 1 0.1424 392459.200 4 3 1 0.1367 456892.800 5 1 1 0.1360 284512.000 6 1 1 0.1080 307105.600 7 2 1 0.1080 307105.600 8 3 1 0.1080 307105.600 9 4 1 0.1490 334720.000 10 9 1 0.1229 476976.000 11 9 1 0.1090 284512.000 5 4 1 0.1360 284512.000 [angles] ; ai aj ak funct c0 c1 c2 c3 1 2 3 1 107.300 585.760 2 3 4 1 107.300 585.760 2 1 5 1 110.600 585.760 2 1 6 1 132.100 292.880 1 2 7 1 125.700 292.880 2 3 8 1 127.500 292.880 3 4 9 1 120.000 711.280 4 9 10 1 120.400 669.440 4 9 11 1 115.000 292.880 1 5 4 1 106.500 585.760 4 3 8 1 125.700 292.880 5 1 6 1 113.400 292.880 3 2 7 1 127.500 292.880 5 4 9 1 120.360 513.377 10 9 11 1 123.000 292.880 3 4 5 1 110.600 585.760 [dihedrals] ; IMPROPER DIHEDRAL ANGLES ; ai aj ak al funct c0 c1 c2 c3 c4 c5 9 4 3 5 4 180.000 10.460 2 8 3 2 4 4 180.000 10.460 2 7 2 1 3 4 180.000 10.460 2 6 1 2 5 4 180.000 10.460 2 11 9 4 10 4 180.000 43.932 2 [dihedrals] ; PROPER DIHEDRAL ANGLES ; ai aj ak al funct c0 c1 c2 c3 c4 c5 9 4 3 2 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 9 4 3 8 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 9 4 5 1 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 3 4 5 1 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 4 3 2 1 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 4 5 1 2 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 8 3 2 1 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 7 2 3 4 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 8 3 2 7 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 7 2 1 6 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 8 3 4 5 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 7 2 1 5 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 6 1 2 3 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 6 1 5 4 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 11 9 4 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 11 9 4 5 3 0.000 0.000 0.000 -0.000 -0.000 0.000 10 9 4 3 3 7.845 -1.569 -6.276 -0.000 -0.000 0.000 10 9 4 5 3 4.707 1.569 -6.276 -0.000 -0.000 0.000 5 1 2 3 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 5 4 3 2 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 [pairs] 3 6 1 1 8 1 4 6 1 1 9 1 4 7 1 2 9 1 5 7 1 6 7 1 5 8 1 3 10 1 3 11 1 7 8 1 5 10 1 5 11 1 8 9 1 * * * ;furfural.rtp ; [FUR] [atoms] C1 opls\_567 -0.0710 1 C2 opls\_568 -0.2599 1 C3 opls\_568 -0.1782 1 C4 opls\_567 -0.1566 1 O1 opls\_566 -0.0507 1 H1 opls\_569 0.2330 1 H2 opls\_570 0.1877 1 H3 opls\_570 0.1861 1 C5 opls\_141 0.3431 1 O2 opls\_278 -0.3782 1 H4 opls\_140 0.1447 1 [bonds] C2 C1 0.1367 456892.800 C3 C2 0.1424 392459.200 C4 C3 0.1367 456892.800 O1 C1 0.1360 284512.000 H1 C1 0.1080 307105.600 H2 C2 0.1080 307105.600 H3 C3 0.1080 307105.600 C5 C4 0.1490 334720.000 O2 C5 0.1229 476976.000 H4 C5 0.1090 284512.000 O1 C4 0.1360 284512.000 [angles] ; ai aj ak th0 cth C1 C2 C3 107.300 585.760 C2 C3 C4 107.300 585.760 C2 C1 O1 110.600 585.760 C2 C1 H1 132.100 292.880 C1 C2 H2 125.700 292.880 C2 C3 H3 127.500 292.880 C3 C4 C5 120.000 711.280 C4 C5 O2 120.400 669.440 C4 C5 H4 115.000 292.880 C1 C5 C4 106.500 585.760 C4 C3 H3 125.700 292.880 O1 C1 H1 113.400 292.880 C3 C2 H2 127.500 292.880 O1 C4 C5 120.360 513.377 O2 C5 H4 123.000 292.880 C3 C4 O1 110.600 585.760 [dihedrals] ; IMPROPER DIHEDRAL ANGLES ; ai aj ak al q0 cq c3 C5 C4 C3 O1 180.000 10.460 2 H3 C3 C2 C4 180.000 10.460 2 H2 C2 C1 C3 180.000 10.460 2 H1 C1 C2 O1 180.000 10.460 2 H4 C5 C4 O2 180.000 43.932 2 ## [dihedrals] ; PROPER DIHEDRAL ANGLES ; ai aj ak al c0 c1 c2 c3 c4 c5 C5 C4 C3 C2 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 C5 C4 C3 H3 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 C5 C4 O1 C1 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 C3 C4 O1 C1 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 C4 C3 C2 C1 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 C4 O1 C1 C2 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 H3 C3 C2 C1 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 H2 C2 C3 C4 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 H3 C3 C2 H2 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 H2 C2 C1 H1 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 H3 C3 C4 O1 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 H2 C2 C1 O1 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 H1 C1 C2 C3 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 H1 C1 O1 C4 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 H4 C5 C4 C3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 H4 C5 C4 O1 3 0.000 0.000 0.000 -0.000 -0.000 0.000 O2 C5 C4 C3 3 7.845 -1.569 -6.276 -0.000 -0.000 0.000 O2 C5 C4 O1 3 4.707 1.569 -6.276 -0.000 -0.000 0.000 O1 C1 C2 C3 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 O1 C4 C3 C2 3 30.334 0.000 -30.334 -0.000 -0.000 0.000 Here is the error: Processing chain 1 (11 atoms, 1 residues) Warning: Starting residue FUR0 in chain not identified as Protein/RNA/DNA. 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 11 atoms Making bonds… Warning: Long Bond (2-1 = 0.922267 nm) Warning: Long Bond (3-2 = 0.527986 nm) Warning: Long Bond (4-3 = 0.304304 nm) Warning: Long Bond (5-1 = 0.336149 nm) Warning: Long Bond (6-1 = 0.423567 nm) Warning: Long Bond (7-2 = 1.06552 nm) Warning: Long Bond (8-3 = 0.450706 nm) Warning: Long Bond (9-4 = 0.64842 nm) Warning: Long Bond (10-9 = 0.501155 nm) Warning: Long Bond (11-9 = 0.809707 nm) Warning: Long Bond (5-4 = 0.41183 nm) Number of bonds was 11, now 11 Generating angles, dihedrals and pairs… Before cleaning: 15 pairs Before cleaning: 20 dihedrals Making cmap torsions… There are 20 dihedrals, 0 impropers, 17 angles 15 pairs, 11 bonds and 0 virtual sites Total mass 96.086 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file… --------- PLEASE NOTE ------------ You have successfully generated a topology from: furfural.pdb. The Oplsaa force field and the tip4p water model are used. --------- ETON ESAELP ------------ GROMACS reminds you: “Love is Like Moby Dick, Get Chewed and Get Spat Out” (Urban Dance Squad) * * * I’ve tried using x2top, but i get this error, which makes sense, _ **Fatal error: Could only find a forcefield type for 1 out of 11 atoms** _ I’ve not found any necessary info to be able to add to the atomname2type.n2t file to potentially correct this error from x2top. I’m unsure if I’m going about the whole process all wrong, but any help would be greatly appreciated! Thanks ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [March 21, 2024, 3:26pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-long-bond-warning/8664/2 "2024-03-21T15:26:22Z")
You need to paramterise non-standard molecule. ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [March 21, 2024, 3:28pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-long-bond-warning/8664/3 "2024-03-21T15:28:19Z")
Is the PDB file you show the exact copy of your file? Or is it the forum that has automatically removed spaces, making the columns wrong? ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [March 21, 2024, 3:33pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-long-bond-warning/8664/4 "2024-03-21T15:33:15Z")
[Generation of topology for non-standard molecules](https://gromacs.bioexcel.eu/t/generation-of-topology-for-non-standard-molecules/2789) might help you as well. ---
**Author:** ![lcole3](https://avatars.discourse-cdn.com/v4/letter/l/3be4f8/32.png) [@lcole3](https://gromacs.bioexcel.eu/u/lcole3)\ **Post date:** [March 21, 2024, 6:35pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-long-bond-warning/8664/5 "2024-03-21T18:35:43Z")
It’s the forum