Residue type 'DA5' not found in residue topology database

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1

GROMACS version: 2021.4
GROMACS modification: No
Force field: CHARMM36
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I am trying to simulate a double-stranded DNA using CHARMM36 force field, but I am encountering the error " Residue type not found in residue topology database". The wholescreen is attached. Thanks in advance.

gmx pdb2gmx -f 0s_6nm_clean.pdb -o Os_6nm__processed.gro -water spce
:-) GROMACS - gmx pdb2gmx, 2021.4-Ubuntu-2021.4-2 (-:

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GROMACS: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/nm/projects
Command line:
gmx pdb2gmx -f 0s_6nm_clean.pdb -o Os_6nm__processed.gro -water spce

Select the Force Field:

From current directory:

1: CHARMM all-atom force field

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 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9)

16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
1

Using the Charmm36-jul2022 force field in directory ./charmm36-jul2022.ff

going to rename ./charmm36-jul2022.ff/aminoacids.r2b
Opening force field file ./charmm36-jul2022.ff/aminoacids.r2b

going to rename ./charmm36-jul2022.ff/carb.r2b
Opening force field file ./charmm36-jul2022.ff/carb.r2b

going to rename ./charmm36-jul2022.ff/cgenff.r2b
Opening force field file ./charmm36-jul2022.ff/cgenff.r2b

going to rename ./charmm36-jul2022.ff/ethers.r2b
Opening force field file ./charmm36-jul2022.ff/ethers.r2b

going to rename ./charmm36-jul2022.ff/lipid.r2b
Opening force field file ./charmm36-jul2022.ff/lipid.r2b

going to rename ./charmm36-jul2022.ff/metals.r2b
Opening force field file ./charmm36-jul2022.ff/metals.r2b

going to rename ./charmm36-jul2022.ff/na.r2b
Opening force field file ./charmm36-jul2022.ff/na.r2b

going to rename ./charmm36-jul2022.ff/silicates.r2b
Opening force field file ./charmm36-jul2022.ff/silicates.r2b

going to rename ./charmm36-jul2022.ff/solvent.r2b
Opening force field file ./charmm36-jul2022.ff/solvent.r2b
Reading 0s_6nm_clean.pdb…
Read ‘’, 3054 atoms

Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.

There are 2 chains and 0 blocks of water and 96 residues with 3054 atoms

chain #res #atoms

1 ‘A’ 48 1530

2 ‘B’ 48 1524

All occupancies are one
All occupancies are one
Opening force field file ./charmm36-jul2022.ff/atomtypes.atp

Reading residue database… (Charmm36-jul2022)
Opening force field file ./charmm36-jul2022.ff/aminoacids.rtp
Opening force field file ./charmm36-jul2022.ff/carb.rtp
Opening force field file ./charmm36-jul2022.ff/cgenff.rtp
Opening force field file ./charmm36-jul2022.ff/ethers.rtp
Opening force field file ./charmm36-jul2022.ff/lipid.rtp
Opening force field file ./charmm36-jul2022.ff/metals.rtp
Opening force field file ./charmm36-jul2022.ff/na.rtp
Opening force field file ./charmm36-jul2022.ff/silicates.rtp
Opening force field file ./charmm36-jul2022.ff/solvent.rtp
Opening force field file ./charmm36-jul2022.ff/aminoacids.hdb
Opening force field file ./charmm36-jul2022.ff/carb.hdb
Opening force field file ./charmm36-jul2022.ff/cgenff.hdb
Opening force field file ./charmm36-jul2022.ff/ethers.hdb
Opening force field file ./charmm36-jul2022.ff/lipid.hdb
Opening force field file ./charmm36-jul2022.ff/metals.hdb
Opening force field file ./charmm36-jul2022.ff/na.hdb
Opening force field file ./charmm36-jul2022.ff/silicates.hdb
Opening force field file ./charmm36-jul2022.ff/solvent.hdb
Opening force field file ./charmm36-jul2022.ff/aminoacids.n.tdb
Opening force field file ./charmm36-jul2022.ff/carb.n.tdb
Opening force field file ./charmm36-jul2022.ff/cgenff.n.tdb
Opening force field file ./charmm36-jul2022.ff/ethers.n.tdb
Opening force field file ./charmm36-jul2022.ff/lipid.n.tdb
Opening force field file ./charmm36-jul2022.ff/metals.n.tdb
Opening force field file ./charmm36-jul2022.ff/na.n.tdb
Opening force field file ./charmm36-jul2022.ff/silicates.n.tdb
Opening force field file ./charmm36-jul2022.ff/solvent.n.tdb
Opening force field file ./charmm36-jul2022.ff/aminoacids.c.tdb
Opening force field file ./charmm36-jul2022.ff/carb.c.tdb
Opening force field file ./charmm36-jul2022.ff/cgenff.c.tdb
Opening force field file ./charmm36-jul2022.ff/ethers.c.tdb
Opening force field file ./charmm36-jul2022.ff/lipid.c.tdb
Opening force field file ./charmm36-jul2022.ff/metals.c.tdb
Opening force field file ./charmm36-jul2022.ff/na.c.tdb
Opening force field file ./charmm36-jul2022.ff/silicates.c.tdb
Opening force field file ./charmm36-jul2022.ff/solvent.c.tdb

Processing chain 1 ‘A’ (1530 atoms, 48 residues)

Identified residue DA51 as a starting terminus.

Identified residue DG348 as a ending terminus.

Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 624)

Fatal error:
Residue type ‘DA5’ not found in residue topology database

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

2

It should help if you rename your 5’-terminal residues from e.g. DA5 to DA, and 3’-terminal residues from e.g. DG3 to DG in the pdb. In Gromacs, CHARMM has a different terminal patching protocol than Amber, so they don’t have separately defined DA5/DA3, DG5/DG3, … residues.

3

I tried using that but still error is coming

4

The naming of initial and terminal residues is defined in .r2b files, so you should make sure your ./charmm36-jul2022.ff/na.r2b does not try to rename e.g. DA to DA5 at the 5’-terminal side.

I checked myself, and with the said force field I was able to generate a topology for this random dsDNA structure (adding a .dat) with C7 renamed to C5M and OP1/OP2 to O1P/O2P:
x.pdb.dat (35.3 KB)

just by using the additional -ter keyword to gmx pdb2gmx for interactive termini selection. Try to see if that works for you, and if so, try working backwards from there to fix your particular case.