Dear List,
I was trying to do an MD simulation on a complex consisting of protein, heme, and ligand. I minimized the complex using "tutorial4b" (
https://ambermd.org/tutorials/basic/tutorial4b/) and then performed min and heat steps on the complex using "tutorial3" (
https://ambermd.org/tutorials/advanced/tutorial3/section1.php). I encountered the following error when doing the "density" step:
Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM.
It seems that there are some problems with my prmtop and rst files, or maybe the original pdb file, which I prepared in the previous step.
Best regards,Siavoush
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Received on Thu Dec 11 2025 - 05:00:10 PST
