Hi. This is in context of protein-protein simulation.One of my protein is a 167 residue chain(receptor), the other protein is a 41 residue peptide (ligand). I am using mindist with the -or option to see how my ligand comes close to my receptor protein.
I have the following questions: 1) When we say minimum distances ( my index file has atoms of ligand saved as ligand and receptor atoms saved as receptor, I am calculating mindist between these two groups), what exactly is being calculated? Does it mean the minimum distance from any atom of ligand to any atom of the receptor? 2)Can anybody clarify more on the phrase " minimum distances to each residue in the first group are determined and plotted as a function of residue number." ? 3) Minimum distance is being calculated between which quantity? (e.g C-alpha or Centre of Mass ?) and finally , is my approach correct for my system? Regards, Sampurna -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.