GROMACS version: 2024.1
GROMACS modification: Yes/No
Hello Gromacs users,
I’m new to Gromacs and only had limited experience in protein works. I’m recently trying to use Amber’s OL21 forcefield for some DNA oligomer simulations. Initially both of the 5’ terminus had a phosphate group, so I manually changed it to OH. To match the dna.rpt file in forcefield, I renamed the new H in pdb file as H5T. I then started to generate a topology file with pdb2gmx, but it gave me this error message and stopped. Does anyone know what happened? What should I do to fix it? Thank you.
Processing chain 1 ‘A’ (162 atoms, 8 residues)
Identified residue DA1 as a starting terminus.
Identified residue DT8 as a ending terminus.
9 out of 9 lines of specbond.dat converted successfully
Opening force field file ./amber14sb_OL21.ff/aminoacids.arn
Opening force field file ./amber14sb_OL21.ff/dna.arn
Opening force field file ./amber14sb_OL21.ff/rna.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Segmentation fault
This is what’s inside rna.arn:
RNA OP1 O1P
RNA OP2 O2P
RNA H2’ H2’1
RNA H2’’ H2’2
RNA H5’ H5’1
RNA H5’’ H5’2
RNA HO5’ H5T
RNA HO3’ H3T