PDB2GMX for Modified DNA_CHAIN

GROMACS version: GROMACS 2021.3-foss-2021a
GROMACS modification: Yes/No
I’m trying to generate a topology for a modified DNA strand using CHARMM27. This modified DNA strand has an abasic site in the middle of the strand and a ligated chemical moiety to that abasic site. The moiety is written in the PDB file under ‘UNK’ and appears after the listed DNA residues/(bases) listed, this is not the cause of my issue. The cause of my issue is the abasic site, it’s listed as -8DT and being an abasic site lacks the constituent atoms of a thymine residue.

I, therefore, receive the error:

Fatal error:
Atom H01 in residue DT -8 was not found in rtp entry DT with 32 atoms
while sorting atoms.

I tried -missing option but to no avail. Would greatly appreciate any advice on overcoming this issue and creating the topology file.

On a side note, is it possible to form the topology for a duplex and not have to do each strand as a separate pdb file?

many thanks for your reply!

Please share the files because this much information doesn’t help us.

None of the force fields in GROMACS know what an abasic site is. You will have to create your own .rtp entry for it with the base excised. Some force fields may support this (CHARMM does, I’m not sure about others).

Thanks for your reply! I’m trying to use CHARMM.

I attempted “-rtpo” but received the following error:
“Error in user input:
Invalid command-line options
Unknown command-line option -rtpo”

in parallel I found the CHARMM dna.rtp: it lists the residue names like:
[ DT ]
as my abasic site DT residue but is the -8 DT specifically can I specify something like [-8 DT] or indeed call it something else all together in the PDB file “ABASIC” the reference a section in the .rtp like: [ABASIC]?

You need a new residue definition. The residue number is irrelevant. “ABASIC” is too long for PDB standard, so you need something that is 4 characters or less. Here’s a useful reference for doing this: https://manual.gromacs.org/current/how-to/topology.html