There should be a log file created by ante-MMPBSA.py that writes out more error information that would be helpful for diagnosis. Without that, it’s difficult to ascertain what might be wrong here.
-Bill
> On May 4, 2025, at 11:51 AM, Righteous via AMBER <amber.ambermd.org> wrote:
>
> 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.
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Received on Sun May 04 2025 - 10:00:02 PDT
