[gmx-users] Distance matrix between chains

[Clarke, Benjamin (NIH/NIDDK) [F]]

Dear all,

I am analyzing a MD trajectory of a protein heterodimer and would like to identify dimer interface residues.  I have used


gmx mdmat -f md_noPBC.xtc -s md.tpr

Select Group 9 (SideChain-H)

gmx xpm2ps -f dm.xpm -o dm.eps


to create a distance matrix of all residue-residue interactions.  This is OK, but I would prefer to report just inter-Chain interactions.  Is this possible to make this with “mdmat”?  Can I plot Chain A on the y-axis and Chain B on the x-axis?


Thanks,

Ben Clarke