I’m getting a puzzling result with cpptraj. I run an MD on a long polysaccharide, I then run a cpptraj script to load the parm file and trajectory (I run in octahedral cell with water but save only the PS), calculate the distance between the extremes (distance r2to60 :2 :60 out r.dat) and save the selected frames as pdb in the same process. Next, I load the pdb trajectory and calculate the same distance (as L1), the result is different (but correct). The latter calculation is the correct one, I can load the trajectory as PDB or .nc in Pymol and confirm the result.
I run out of ideas what I could do different, please, advise.
First lines of distances:
#Frame L1 #Frame r2to60
1 81.0188 1 41.0548
2 81.5262 2 40.7852
3 83.2191 3 40.6565
4 77.5096 4 48.3777
5 75.7135 5 49.6401
6 70.3752 6 53.8676
7 68.1719 7 58.3595
8 67.3075 8 59.0428
9 64.6456 9 58.7674
…
Thanks,
Hugo
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Received on Tue Mar 14 2023 - 11:00:03 PDT
