I'm not seeing the first message in the amber archive. Nor can I find it in my email folder. This is likely the first time most/any of us are seeing it. You say the pdb was generated with tleap. Was the crd also generated with tleap? Or is it the result of a minimization? A simulation? In what ensemble? Is there an input file? You mention that you were "analyzing" the coordinates; does this mean the crd file was generated from cpptraj or pytraj? It's unclear what programs you are using (e.g., tleap, sander, sander.MPI, pmemd, pmemd.cuda, etc), nor is it clear what procedure one must follow to reproduce the issue. You asked about visualization artifacts; however, we can't see the image and it's unclear how you are visualizing it. This is unlikely to be resolved without additional information.
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Received on Wed Aug 06 2025 - 07:30:03 PDT
