Dear Amber community,
While using cpptraj to measure RMSD and distance between 2 separate structure files (a protein-ligand complex, one being the crystal pose one being a built model with different pose), when I had the protein aligned to each other, the RMSD of the total CA is close to 0 as expected. So should the ligand, for my set of selected atoms (because they are), but the ligand RMSD values are way off. Wasn’t the first time I ran into this problem-previously when I chose the atoms pairs one by one on each input line and dataset, and manually calculate the combined RMSD, the problem seemed to go to away. But not this time.
I ran a lot of tests, and eventually simplified the file inputs into 2 pdb files only, so no .prmtop files to match up to each structure.
Finally, it was found that because the built model had the ligand atoms in a different order than the crystal reference (but atom names were identical), even though I defined all the atoms in cpptraj by “ :residue.atomname “ , what cpptraj did was it took in the atom number from the target based on the atom name, and tried to correspond it to the same atom number in the reference-which in my case is a different atom.
This behavior I didn’t find someone mention online or in the manual-don’t know if I missed something. One would expect the atom name to correspond to atom name-and the terminal output on screen shows the atoms based on the input names with no mention of the true atoms it’s measuring.
It’d be great if there’s a way for cpptraj to correspond atom names regardless of their sequence within a residue, otherwise not just atom names, but also atom sequences have to be identical in the initial PDBs from model building, in order to use it to do RMSD and distance calculations.
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Received on Fri Apr 09 2021 - 14:00:02 PDT
