Hi experts.
When using the distance command ( I have kept the imaging to off) I am not sure if the distance masks are being read correctly, I want to calculate the distance between the O22 atom of RES ligand to the N6 atom of the adenine and I am not sure if this is working. The distances on pymol are in the range of ~2 to 3 angstroms but when I open the dat file it is ~ 60 angstroms or more.
Secondly I wanted to use the first frame as reference instead of using the solvated initial setup.pdb file but when I plugged in "reference first" it did not like me either.
Any suggestions on what I am missing ?
cpptraj command I am using after loading the traj and stripping water and ions:
distance d1 :RES.O22 :3.N6 noimage reference out d1_ligand.dat
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 11 2024 - 10:00:02 PDT
