GROMACS version: 2025.3
GROMACS modification: No
Long time lurker. First time I’ve felt the need to make an account to jump in with a question of my own that I couldn’t solve with existing questions here. These forums have been invaluable and the folks here are always so helpful. :)
This is my first simulation that I’m attempting using Amber14SB force field (along with TIP4P-D water model) of a protein in 0.15M NaCL solution. I encountered this error when trying to run grompp just after adding solvate to the system:
ERROR 1 [file topol.top, line 31435]:
No default Per. Imp. Dih. types for interaction
‘2729 2732 2738 2733 4’.
Based on the error text, this is due to missing dihedral interactions. This is a HIS residue involved from checking my topology file with grep:
2729 CT 161 HIS CB 2729 -0.0462 12.01
2732 CC 161 HIS CG 2732 -0.0266 12.01
2733 NA 161 HIS ND1 2733 -0.3811 14.01
2738 CV 161 HIS CD2 2738 0.1292 12.01
This all lead me to make a new itp file with the following lines and include them in the amber14SB ffbonded.itp file. The numbers were copied from those in the amber14SB file:
[ dihedraltypes ] ; improper
;i j k l func phase kd pn
CT CC CV NA 4 180.00 4.60240 2
CC CV NA CR 4 180.00 4.60240 2
CV NA CR NB 4 180.00 4.60240 2
Adding those lines fixed it and the simulation can be run. Is this correct reason for the error and if yes, is my “fix” the correct way to do it or is there a better, more robust, way? Want to make sure my understanding is correct and the solution is sound. Thank you so much!