GROMACS version:2021.4
GROMACS modification: No
Hi, I’m currently learning how to do MD analysis by myself and after following the instructions on the Gromacs tutorial page, I wanted to do a MD analysis by myself but the ligand, Omipalisib, gives me high penalty score when I form topology file in the system.
| Uploaded Mol2 | : unk_fix.mol2 |
|---|---|
| Job Name | : unk_fix |
| Options Selected | : |
- Output Mol2
- Include Warnings
- Include Debug Info
| Param Penalty | : 213.500 |
|---|---|
| Charge Penalty | : 76.732 |
The FFParam program can be used to facilitate the optimization of parameters for molecules with high “Param” and/or “Charge” penalties. Visit FFParam to learn more.
I’m also new into bioinformatics so please can you explain it to me what I should do with step by step. Thank you.