Pdb2gmx does not recognize DNA when used with Force Field 'charm36-jul2022'

User discussions
1

GROMACS version: 2022.4
GROMACS modification: No
My questions are below. Here is a bit of background:

I have run successfully pdb2gmx with the Force Field ‘amber03’. The pdb entry is 5kkq
I have downloaded the Force Field ‘charm36-jul2022’ and it throws an error while trying to read the DNA within 5kkq …
'Fatal error:
atom N not found in building block 1DT while combining tdb and rtp

  1. Has anyone else had problems with ‘charm36’?
  2. My friend Vis K. suggested that I add the option -ter to the command containing pdb2gmx but I would like to find an answer that does not involve manual inputs as we are planning to automate this process.
    Does anyone have additional suggestions?
  3. Is there a way to add ‘charm36-jul2022’ to the GROMACS installation directory? Would this solve this issue?
    Thank you in advance !
    CHF
2

You need to manually select termini whenever using the CHARMM36 force field. You can automate this via echo like any other non-interactive selection in GROMACS.

3

Thank you for your reply: quite helpful