Atom C7 in residue DT 3 was not found in rtp entry DT with 32 atoms while sorting atoms

User discussions
1

Hello,

I am getting the following error during pdb2gmx.

Fatal error: Atom C7 in residue DT 3 was not found in rtp entry DT with 32 atoms while sorting atoms.
while preparing topology file for DNA.

I checked the pdb file and ffopls.rtp file also.

jahanvi

2

What did you find? Your PDB file names an atom in a way that is not consistent with what the force field expects.

3

hello sir,

I appreciate your response and assistance.
After thoroughly analysing the terminal error, I attempted to replace C7 with C5M within the topology file. this was successfully accomplished.
Am I able to make this change?
I have attached my PDB file link for your review and would appreciate your assistance in checking it.

Jahanvi