GROMACS version: 2023
GROMACS modification: Yes/No
I have been trying to troubleshoot and perform the simulation for my designed peptide with the drug, however since gromacs does not directly recognise drug, so I generated the topolgy files for my drug using the antechamber and acpype (ambertools 24). However, even after generating the .itp, .top and .gro files for the drug , my gromacs is not recognising the drug and is removing it in complex simulation, i have made the necessary changes in log files to incorporate the ligand.itp in the files. Tried troubleshooting and using other ffs such as gromos, however, the error persists and gromacs doesnt recognise my drug, how do I proceed. Kindly guide me, I’m new to this field. Thankyou in advance.
P.S. i have been using the docked complex of my peptide and drug.