How to perform Protein-DNA simulation using CHARMM36

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1

GROMACS version: 2018.x
GROMACS modification: Yes/No
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I want to simulate a Protein-DNA complex using CHARMM36 forcefield. I am not able to generate topology file using pdb2gmx command. I am getting an error
Fatal error:
Atom C7 in residue DT 1 was not found in rtp entry DT with 30 atoms
while sorting atoms.
Can anyone please tell me how can I proceed

2

Hi, thymine is notorious for inconsistencies in atom naming. In CHARMM, the methyl carbon is called C5M instead of C7, so a quick substitution should fix that.

Remember to keep the number of fields constant though, PDB is a fixed format.

3

Thank you! Again I am getting a similar error for different atom.
This is what I selected for start and end terminus
Select start terminus type for DT-1
0: 5TER
1: 5MET
2: 5PHO
3: 5POM
4: None
0
Start terminus DT-1: 5TER
Select end terminus type for DT-8
0: 3TER
1: None
0
End terminus DT-8: 3TER
Opening force field file ./charmm36-jul2022.ff/aminoacids.arn

Program gmx_mpi, VERSION 5.0.4
Source code file: /opt/compile/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 732

Fatal error:
Atom OP1 in residue DC 2 was not found in rtp entry DC with 30 atoms
while sorting atoms.

4

It looks like a similar discrepancy, OP1/OP2 vs O1P/O2P.

If you don’t want to struggle with these things over and over, you might want to create an .arn file in the respective FF directory (same core name as the .rtp that contains DNA residue definitions), with content resembling the following:

DNA  OP1  O1P
DNA  OP2  O2P
DNA   C7  C5M
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