Urgent: Queries regarding the gromacs file synthesis for DNA-lipid systems

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GROMACS version: 2023.4
GROMACS modification: Yes/No
Here post your question
Command line:
gmx pdb2gmx -f new.pdb -o dna_chl.gro -ter -ignh
Making bonds…

Number of bonds was 410, now 410

Generating angles, dihedrals and pairs…
Before cleaning: 992 pairs
Before cleaning: 1082 dihedrals

Making cmap torsions…

There are 1082 dihedrals, 32 impropers, 744 angles
956 pairs, 410 bonds and 0 virtual sites

Total mass 3633.382 a.m.u.

Total charge -11.000 e

Writing topology

Back Off! I just backed up posre_DNA_chain_D.itp to ./#posre_DNA_chain_D.itp.10#

Processing chain 2 ‘B’ (48 atoms, 1 residues)

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
Opening force field file ./charmm36-jul2022.ff/aminoacids.arn

Checking for duplicate atoms…

Generating any missing hydrogen atoms and/or adding termini.

Now there are 1 residues with 48 atoms
Chain time…

Back Off! I just backed up topol_Other_chain_B.itp to ./#topol_Other_chain_B.itp.10#

Making bonds…

atom H41A is missing in residue 3CHL 36 in the pdb file

atom H41A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H41A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H41A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H41B is missing in residue 3CHL 36 in the pdb file

atom H41B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H41B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H41B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H40 is missing in residue 3CHL 36 in the pdb file

atom H40 is missing in residue 3CHL 36 in the pdb file

You might need to add atom H40 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H40 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H40H is missing in residue 3CHL 36 in the pdb file

atom H40H is missing in residue 3CHL 36 in the pdb file

You might need to add atom H40H to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H40H to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H39A is missing in residue 3CHL 36 in the pdb file

atom H39A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H39A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H39A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H39B is missing in residue 3CHL 36 in the pdb file

atom H39B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H39B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H39B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H38A is missing in residue 3CHL 36 in the pdb file

atom H38A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H38A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H38A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H38B is missing in residue 3CHL 36 in the pdb file

atom H38B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H38B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H38B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H37A is missing in residue 3CHL 36 in the pdb file

atom H37A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H37A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H37A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H37B is missing in residue 3CHL 36 in the pdb file

atom H37B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H37B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H37B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H36A is missing in residue 3CHL 36 in the pdb file

atom H36A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H36A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H36A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H36B is missing in residue 3CHL 36 in the pdb file

atom H36B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H36B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H36B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H35A is missing in residue 3CHL 36 in the pdb file

atom H35A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H35A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H35A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H35B is missing in residue 3CHL 36 in the pdb file

atom H35B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H35B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H35B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H34A is missing in residue 3CHL 36 in the pdb file

atom H34A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H34A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H34A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H34B is missing in residue 3CHL 36 in the pdb file

atom H34B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H34B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H34B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H33A is missing in residue 3CHL 36 in the pdb file

atom H33A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H33A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H33A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H33B is missing in residue 3CHL 36 in the pdb file

atom H33B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H33B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H33B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H32A is missing in residue 3CHL 36 in the pdb file

atom H32A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H32A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H32A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H32B is missing in residue 3CHL 36 in the pdb file

atom H32B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H32B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H32B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H3 is missing in residue 3CHL 36 in the pdb file

atom H3 is missing in residue 3CHL 36 in the pdb file

You might need to add atom H3 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H3 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H29 is missing in residue 3CHL 36 in the pdb file

atom H29 is missing in residue 3CHL 36 in the pdb file

You might need to add atom H29 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H29 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H30A is missing in residue 3CHL 36 in the pdb file

atom H30A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H30A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H30A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H30B is missing in residue 3CHL 36 in the pdb file

atom H30B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H30B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H30B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H31A is missing in residue 3CHL 36 in the pdb file

atom H31A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H31A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H31A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H31B is missing in residue 3CHL 36 in the pdb file

atom H31B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H31B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H31B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H4A is missing in residue 3CHL 36 in the pdb file

atom H4A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H4A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H4A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H4B is missing in residue 3CHL 36 in the pdb file

atom H4B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H4B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H4B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H6 is missing in residue 3CHL 36 in the pdb file

atom H6 is missing in residue 3CHL 36 in the pdb file

You might need to add atom H6 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H6 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H7A is missing in residue 3CHL 36 in the pdb file

atom H7A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H7A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H7A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H7B is missing in residue 3CHL 36 in the pdb file

atom H7B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H7B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H7B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H8 is missing in residue 3CHL 36 in the pdb file

atom H8 is missing in residue 3CHL 36 in the pdb file

You might need to add atom H8 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H8 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H14 is missing in residue 3CHL 36 in the pdb file

atom H14 is missing in residue 3CHL 36 in the pdb file

You might need to add atom H14 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H14 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H15A is missing in residue 3CHL 36 in the pdb file

atom H15A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H15A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H15A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H15B is missing in residue 3CHL 36 in the pdb file

atom H15B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H15B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H15B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H16A is missing in residue 3CHL 36 in the pdb file

atom H16A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H16A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H16A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H16B is missing in residue 3CHL 36 in the pdb file

atom H16B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H16B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H16B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H17 is missing in residue 3CHL 36 in the pdb file

atom H17 is missing in residue 3CHL 36 in the pdb file

You might need to add atom H17 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H17 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H18A is missing in residue 3CHL 36 in the pdb file

atom H18A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H18A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H18A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H18B is missing in residue 3CHL 36 in the pdb file

atom H18B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H18B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H18B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H18C is missing in residue 3CHL 36 in the pdb file

atom H18C is missing in residue 3CHL 36 in the pdb file

You might need to add atom H18C to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H18C to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H12A is missing in residue 3CHL 36 in the pdb file

atom H12A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H12A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H12A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H12B is missing in residue 3CHL 36 in the pdb file

atom H12B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H12B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H12B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H11A is missing in residue 3CHL 36 in the pdb file

atom H11A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H11A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H11A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H11B is missing in residue 3CHL 36 in the pdb file

atom H11B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H11B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H11B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H9 is missing in residue 3CHL 36 in the pdb file

atom H9 is missing in residue 3CHL 36 in the pdb file

You might need to add atom H9 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H9 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H19A is missing in residue 3CHL 36 in the pdb file

atom H19A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H19A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H19A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H19B is missing in residue 3CHL 36 in the pdb file

atom H19B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H19B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H19B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H19C is missing in residue 3CHL 36 in the pdb file

atom H19C is missing in residue 3CHL 36 in the pdb file

You might need to add atom H19C to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H19C to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H1A is missing in residue 3CHL 36 in the pdb file

atom H1A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H1A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H1A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H1B is missing in residue 3CHL 36 in the pdb file

atom H1B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H1B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H1B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H2A is missing in residue 3CHL 36 in the pdb file

atom H2A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H2A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H2A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H2B is missing in residue 3CHL 36 in the pdb file

atom H2B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H2B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H2B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H20 is missing in residue 3CHL 36 in the pdb file

atom H20 is missing in residue 3CHL 36 in the pdb file

You might need to add atom H20 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H20 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H21A is missing in residue 3CHL 36 in the pdb file

atom H21A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H21A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H21A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H21B is missing in residue 3CHL 36 in the pdb file

atom H21B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H21B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H21B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H21C is missing in residue 3CHL 36 in the pdb file

atom H21C is missing in residue 3CHL 36 in the pdb file

You might need to add atom H21C to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H21C to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H22A is missing in residue 3CHL 36 in the pdb file

atom H22A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H22A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H22A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H22B is missing in residue 3CHL 36 in the pdb file

atom H22B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H22B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H22B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H23A is missing in residue 3CHL 36 in the pdb file

atom H23A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H23A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H23A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H23B is missing in residue 3CHL 36 in the pdb file

atom H23B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H23B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H23B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H24A is missing in residue 3CHL 36 in the pdb file

atom H24A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H24A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H24A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H24B is missing in residue 3CHL 36 in the pdb file

atom H24B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H24B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H24B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H25 is missing in residue 3CHL 36 in the pdb file

atom H25 is missing in residue 3CHL 36 in the pdb file

You might need to add atom H25 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H25 to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H26A is missing in residue 3CHL 36 in the pdb file

atom H26A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H26A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H26A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H26B is missing in residue 3CHL 36 in the pdb file

atom H26B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H26B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H26B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H26C is missing in residue 3CHL 36 in the pdb file

atom H26C is missing in residue 3CHL 36 in the pdb file

You might need to add atom H26C to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H26C to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H27A is missing in residue 3CHL 36 in the pdb file

atom H27A is missing in residue 3CHL 36 in the pdb file

You might need to add atom H27A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H27A to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H27B is missing in residue 3CHL 36 in the pdb file

atom H27B is missing in residue 3CHL 36 in the pdb file

You might need to add atom H27B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H27B to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

atom H27C is missing in residue 3CHL 36 in the pdb file

atom H27C is missing in residue 3CHL 36 in the pdb file

You might need to add atom H27C to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

You might need to add atom H27C to the hydrogen database of building block 3CHL in the file 3chl.hdb (see the manual)

Program: gmx pdb2gmx, version 2023.3
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1567)

Fatal error:
There were 70 missing atoms in molecule Other_chain_B, if you want to use this
incomplete topology anyhow, use the option -missing

2

It looks like the forcefield you’re using doesn’t have a .hdb file specifying the hydrogen bonds for 3CHL. Based on some previous posts (Please how can i neutralize the system? - #10 by jalemkul), you may need to either fix the naming convention for hydrogen atoms in the pdb file to match the forcefield or design your own .hdb file to add to the forcefield (https://manual.gromacs.org/current/reference-manual/topologies/pdb2gmx-input-files.html#hydrogen-database)

3

@Karis thank you for your suggestions. But, I am facing another new error of O3’ not included in the input. Although in the .rtp file, O3’ bond with C41 is present. O3’ of Thymine is making a covalent bond with C41 of 3CHL.

gmx pdb2gmx -f A00.pdb -o new1.gro -ter -ignh
:-) GROMACS - gmx pdb2gmx, 2023.3 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/nabanita/projects/DNA_chol/10feb
Command line:
gmx pdb2gmx -f A00.pdb -o new1.gro -ter -ignh

Select the Force Field:

From current directory:

1: CHARMM all-atom force field

2: CHARMM all-atom force field

From ‘/usr/local/gromacs/share/gromacs/top’:

3: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)

4: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)

5: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)

6: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)

7: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)

8: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)

9: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)

10: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)

11: GROMOS96 43a1 force field

12: GROMOS96 43a2 force field (improved alkane dihedrals)

13: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)

14: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)

15: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)

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 Charmm36-jul2022 force field in directory ./charmm36-jul2022.ff
Opening force field file ./charmm36-jul2022.ff/watermodels.dat

Select the Water Model:

1: TIP3P CHARMM-modified TIP3P water model (recommended over original TIP3P)

2: TIP3P_ORIGINAL Original TIP3P water model

3: SPC SPC water model

4: SPCE SPC/E water model

5: TIP5P TIP5P water model

6: TIP4P TIP4P water model

7: TIP4PEW TIP4P/Ew water model

8: None
1

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
Warning: Residue ‘ADE’ already present with type ‘DNA’ in database, ignoring new type ‘RNA’.
Warning: Residue ‘ADE’ already present with type ‘DNA’ in database, ignoring new type ‘RNA’.
Warning: Residue ‘ADE’ already present with type ‘DNA’ in database, ignoring new type ‘RNA’.
Warning: Residue ‘ADE’ already present with type ‘DNA’ in database, ignoring new type ‘RNA’.
Warning: Residue ‘CYT’ already present with type ‘DNA’ in database, ignoring new type ‘RNA’.
Warning: Residue ‘CYT’ already present with type ‘DNA’ in database, ignoring new type ‘RNA’.
Warning: Residue ‘CYT’ already present with type ‘DNA’ in database, ignoring new type ‘RNA’.
Warning: Residue ‘CYT’ already present with type ‘DNA’ in database, ignoring new type ‘RNA’.
Warning: Residue ‘GUA’ already present with type ‘DNA’ in database, ignoring new type ‘RNA’.
Warning: Residue ‘GUA’ already present with type ‘DNA’ in database, ignoring new type ‘RNA’.
Warning: Residue ‘GUA’ already present with type ‘DNA’ in database, ignoring new type ‘RNA’.
Warning: Residue ‘GUA’ already present with type ‘DNA’ in database, ignoring new type ‘RNA’.
Reading A00.pdb…
Read ‘’, 291 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 13 residues with 291 atoms

chain #res #atoms

1 ‘D’ 13 291

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/3chl.hdb
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/3chl.n.tdb
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/3chl.c.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

Back Off! I just backed up topol.top to ./#topol.top.47#

Processing chain 1 ‘D’ (291 atoms, 13 residues)

Identified residue DA51 as a starting terminus.

Identified residue 3CHL13 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for DA5-1
0: 3TER
1: NH3+
2: NH2
3: HYD1
4: MET1
5: 5TER
6: 5MET
7: 5PHO
8: 5POM
9: None
5
Start terminus DA5-1: 5TER
Select end terminus type for 3CHL-13
0: COO-
1: COOH
2: CT2
3: CT1
4: HYD2
5: MET2
6: 3TER
7: None
6
End terminus 3CHL-13: 3TER
Opening force field file ./charmm36-jul2022.ff/aminoacids.arn

Checking for duplicate atoms…

Generating any missing hydrogen atoms and/or adding termini.

Program: gmx pdb2gmx, version 2023.3
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 154)

Fatal error:
Residue 13 named 3CHL of a molecule in the input file was mapped
to an entry in the topology database, but the atom O3 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

4

To clarify, by " O3’ of Thymine is making a covalent bond with C41 of 3CHL", the same oxygen is making covalent bonds with thymine and C41, correct? My understanding is that if there are additional covalent bonds to atoms not included as part of the residue in the topology database, then the residue might not be recognized. Since the O3 is already recognized as part of Thymine, it may not be included when the program is trying to identify whether residue 13 matches with 3CHL. If this is the issue, you could add your own parameters for the thymine bound to CHL as its own residue using tools like CGenFF (similar to what was done for the ligand in this tutorial http://www.mdtutorials.com/gmx/complex/02_topology.html)

5

@Karis thank you for your suggestion. I have a doubt should I take the entire thymine residue along with 3CHL as ligand or should I take the O3’ residue alongwith 3CHL residues for building the str file in CGENFF

P.S. If I am taking the entire thymine with 3CHL, CGENFF is giving the following error
readmol2 warning: skipped unexpected line before @MOLECULE:
@MOLECULE

readmol2 warning: skipped unexpected line before @MOLECULE:
UNL3

readmol2 warning: skipped unexpected line before @MOLECULE:
150 149 0 0 0

readmol2 warning: skipped unexpected line before @MOLECULE:
SMALL

readmol2 warning: skipped unexpected line before @MOLECULE:
GASTEIGER

readmol2 ERROR: @ATOM before @MOLECULE!

Thanks in advance

6

Based off the error you were getting, it seems the forcefield already recognizes that an oxygen should be present on CHL but couldn’t find it due to it being recognized as part of thymine, so you would need to include the entire thymine along with 3CHL to avoid missing atoms in your new topology.

Regarding errors in CGenFF, it may be more helpful to ask the CHARMM forums (https://forums-academiccharmm.org/viewforum.php?f=52&sid=2bdb7d4a0879f00127bd35c8d04b319b)