While adding the force field parameter in dna aptamer

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question
getting these error after running this command - gmx pdb2gmx -f apt02.pdb -o output.gro -ignh
Fatal error:`
Atom O5* in residue DA 1 was not found in rtp entry DA5 with 30 atoms
while sorting atoms.

2

Which force field you are using? check the atom type in the respective files and match that with your pdb

3

I’m using AMBER99sb force field

4

The atom name " O5* " is not defined in the residue DA of AMBER forcefield, which might need to be modified to " O5’ " in the .pdb file. You could check the dna.rtp file in the forcefield’s folder to look up the right atom name in the first column in [atom] part.

[ DA5 ]
[ atoms ]
H5T HO 0.44220 1
O5’ OH -0.63180 2
C5’ CI -0.00690 3
H5’1 H1 0.07540 4
H5’2 H1 0.07540 5
……