GROMACS version: gmx, version 2021.5
GROMACS modification: Yes/No
I’m trying to do a md simulation of a silver nanoparticle capped with Arginine and study it’s interactions with a lipid bilayer. I got the .pdb for Arginine and converted it to .gro using pdb2gmx and adding -ter option at the end. .pdb file only had the -NH group and - C=O group so when I used -ter option it added 1H to the N terminal and an -OH group to the C terminal. These newly added atoms were also included in generated .gro file. I also carried out and energy minimization and an equlibration ( without solvating). The resulting structure was okay and did not show any distortions. Then I capped 100 amino acids to the nanoparticle using packmol and tried to do an energy minimization using water (SPC) as solvent and adding CL to neutralize the charges. But when I try to use the command, “gmx grompp” it gives lots of errors saying " no default angle types and ryckaert-Bell. types" . How do I solve this error? Do I have to add these parameters to the ffbonded.itp? If so where can I find these values? I’m using oplsaa force field. Is there any specific method to follow when using a single amino acid?