Re: ABF FEP with multichain receptor

From: Jérôme Hénin (
Date: Sat Jul 08 2017 - 15:07:36 CDT

Can you send the part of your colvars input that defines the distance


On 8 July 2017 at 18:08, Francesco Pietra <> wrote:

> 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
> $sellig]]]
> 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".
> My first hypothesis was that "cv printframe", for reasons that I do not
> understand, is taking into account the sole chain of the receptor where the
> ligand resides (although even so a 8A is probably not enough. As "cv
> printframe" is wrong about "r", perhaps it is also wrong about Theta, etc--001a114e72c0e19a840553d3e7bd--

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