[gmx-users] g__dist calculate the distance of two residues from different loops

aixintiankong aixintiankong at 126.com
Wed Jun 26 15:32:09 CEST 2013

     when i keep the ligand in the active site,   I use the g_dist calculate  the distance of two residues from two different loops. i look the sticks model of the two residues by pymol and find that there is a gap between the two residues. after using g_dist calculate the distance, i look the distance.xvg file and find that the |d|=0. why? In the pymol i can look the gap, but the distance.xvg show the |d|=0.
     when i remove the ligand  and get the md.xtc, i calculate the distance between the two residues the |d|>1nm.
so i think the ligand can control the Channels opend, this is right or not ?
    And i only want to show teh |d| lines in the distance.xvg, how can i carry out it ?

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