Hello users I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0. Therefore, following Justin's tutorial, I used PRODRG for ligand topolgy. I have drawn ligand using chemdraw and minimized the structure using chem3D. However, during energy minimization step in gromacs, the values converge earlier after 490 steps of minimization. This means that structure is not energy minimized properly. Also, during NVT, it crashes very early giving a LINCS warning which is posted frequently in mailing list and the 'water' molecule not settled error. I have gone through all the solutions and according to my knowledge, the problem is with minimization. I am confused now how to minimize the structure properly to avoid the error. The long bond warning might also arise due to bad minimization? Any suggestions please. If require I can paste the ligand co-ordinates.
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