Dear Amber users and developers,
I am a beginner with Amber. I used CHARMM-GUI to create the necessary files for running Amber simulations. After completing a 500ns simulation, I want to perform MMPBSA analysis on the results. I plan to use ante-MMPBSA.py on the step5_input.prmtop file to obtain the complex topology, receptor topology, and ligand topology after removing water, sodium ions, and chloride ions. Here is my code:
ante-MMPBSA.py -p step5_input.parm7 -c com_nowater.parm7 -r rec_nowater.parm7 -l lig_nowater.parm7 -s ":WAT,Na+,Cl-" -m ":401"
The code returns an error, showing:
Stripping Na+,Cl- (solvent) from original topology, output is com_nowater.parm7
Error: Creating complex topology failed!
How should I resolve this problem? Or what other methods can I use for MMPBSA analysis?
I will appreciate it if someone could give me some suggestions.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun May 04 2025 - 10:00:02 PDT
