From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Jul 08 2017 - 11:08:41 CDT
That helps, thank you.
My question stemmed from observing a major discrepancy for the distance
between the centers of mass of the protein and the ligand according to how
it is measured.
With the same files from a "wrapAll no" MD simulation (just now completed)
loaded to vmd,
set selprot [atomselect top "protein"]
measure center $selprot
set sellig [atomselect top "segname SAA1"]
measure center $sellig
set dist [ veclength [vecsub [measure center $selprot] [measure center
while cv printframe gives 8A, which is totally unrealistic, much too small.
This is just the same that I observed from MD simulations with "wrapAll on"--001a113c552248ec880553d09006--
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