Dear Gromacs users,
I’m intending to simulate a specified protein near two BN sheets.
I added the new residue (BN) in .rtp file and defined the bonding,angles , dihedral and Lenard-Jones parameters in bonded and non bonded files for B and NR atoms.Using Pdb2gmx command, the .gro and .top files were generated including only 2 atoms B and NR.It is supposed that the command considers only one residue in system and ignored the other residues have been bonded together.
I’m wondering if you have any idea where the problem is and how to solve it.
Thanks in advance,
Azar