[gmx-users] how to describe the change of channel in the MD

francesco oteri francesco.oteri at gmail.com
Wed Jun 19 09:49:45 CEST 2013

you can use CAVER (http://www.caver.cz/) to detect tunnels. In the first
case you should not see anything while in the second you shold see a
channel.An other program you can use i s MDPocket ( '
http://bioserv.rpbs.univ-paris-diderot.fr/fpocket/): It simply detects
cavities (either tunnels or closed cavitiies)  and outputs informations.

I successfully used these two software to characterize tunnels and cavities
in a MD simulation.


2013/6/19 aixintiankong <aixintiankong at 126.com>

>  Dear,
>      In the MD, I find that when the ligand keep in the active site , the
> channel formed by two loops is closed. without the ligand the channel is
> opened. I don't know how to describe the change of channel. could i
> describe the channel by calculating the the most narrow distance(mass
> center) between the residues on the two loops? please give me some adviece.
> thank you very much!
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Oteri Francesco, PhD

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