Hi, 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. Francesco 2013/6/19 aixintiankong <aixintiank...@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! > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Oteri Francesco, PhD https://sites.google.com/site/francescooteri -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
