Hello
I'm triying to calculate RMSF of a ligand bound to protein using a crystaline structure as reference. This means i want to alling protein backbone but not the ligand itself as i want to analyze if it's moving within the protein's pocket.
I'm using this input:
parm trayectory.prmtop
parm crystal.prmtop
trajin trayectory.nc 1 -1 1
reference crystal.crd [REF] parm crystal.prmtop
rmsd RMSD :1-578.CA,C,N,O ref [REF] #1-578 is protein only
# if i perform trajout here, backbone allignment is performed correctly
atomicfluct out rmsf_dpg.dat :ligand bymask
run
The problem is that RMSF is performed using first frame, i've checked this by changing trayectory first frame. And changing ligand position in the reference structure doesn't change the result.
Thank you
Martín
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Received on Thu Sep 05 2019 - 08:30:02 PDT
