Re: ABF FEP with multichain receptor

From: Francesco Pietra (
Date: Sat Jul 08 2017 - 11:08:41 CDT

Hi Jerome:
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

gives 28A

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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