Long bond generation

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Hello everyone,
I am trying to make a gro file of ds-DNA attched with modified cholesterol. i have generated the parameters for both. Although the gro file is getting generated, it is forming long and short bonds and changing the structure. It is also saying some residues are missing but those residues are present in .pdb file.
Can anyone help me out in solving the error.
Command line:
gmx pdb2gmx -f dna_chl.gro -o dna_chl.gro -ter -missing

Thanks in advance

This means your coordinate file is either misformatted or has nonsensical atomic positions.

To get assistance with this, please share the entire terminal output from pdb2gmx. It contains a wealth of diagnostic information.

Pro tip: Never use -missing. It only ever leads to trouble :)

@jalemkul Thank you for your suggestions. I am facing problem with hydrogen bond in the 3CHLD, which is my ligand. Although, the hydrogen bonds are present, it is saying missing.
Command: gmx pdb2gmx -f new.pdb -o dna_chl.gro -ter -ignh

@jalemkul any updates on the above missing issue. Please help me out in geenrating the .gro file

pdb2gmx says your starting .pdb does not have the hydrogens (or perhaps has them with different names than in .rtp). If it’s the former, you need to create a .hdb entry for your residue. If the latter, rename the hydrogens; if you have a structure-itp pair, this can be done with Gromologist too,

> p = gml.Pdb('new.pdb', top='topol.itp')
> p.names_from_top()
> p.save_pdb('renamed.pdb')

In addition to the missing H atoms, it seems that your modified residues are defined as occurring in separate chains from the actual DNA itself. You don’t want this, otherwise pdb2gmx will try to generate standalone chains that are not linked to the main DNA.