hi all, I would like to measure the hydrophobic interaction of the ligand against the protein during the simulation . From the forum I learnt g_mindist will be the better tool. But when i used the command g_mindist -f traj.xtc -s topol.tpr -n index.ndx -on numcont.xvg -group and selected protein as group1 and ligand as group 2 i get the result like this
g_mindist -f traj.xtc -s pull.tpr -n index.ndx -on numcont.xvg -group # # g_mindist is part of G R O M A C S: # # Good ROcking Metal Altar for Chronical Sinners # @ title "Number of Contacts < 0.6 nm" @ xaxis label "Time (ps)" @ yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Protein-UNK" 0.000000e+00 21 1.000000e+00 21 2.000000e+00 21 3.000000e+00 21 4.000000e+00 21 5.000000e+00 21 6.000000e+00 21 7.000000e+00 21 8.000000e+00 21 9.000000e+00 21 1.000000e+01 21 1.100000e+01 21 1.200000e+01 21 1.300000e+01 21 1.400000e+01 21 1.500000e+01 21 1.600000e+01 21 1.700000e+01 21 1.800000e+01 21 1.900000e+01 21 2.000000e+01 21 2.100000e+01 21 2.200000e+01 21 2.300000e+01 21 2.400000e+01 21 2.500000e+01 21 2.600000e+01 21 2.700000e+01 21 2.800000e+01 21 2.900000e+01 21 3.000000e+01 21 3.100000e+01 21 3.200000e+01 21 3.300000e+01 21 3.400000e+01 21 3.500000e+01 21 3.600000e+01 21 3.700000e+01 21 3.800000e+01 21 3.900000e+01 21 4.000000e+01 21 4.100000e+01 21 4.200000e+01 21 4.300000e+01 21 4.400000e+01 21 4.500000e+01 21 4.600000e+01 21 4.700000e+01 21 4.800000e+01 21 4.900000e+01 21 5.000000e+01 21 5.100000e+01 21 5.200000e+01 21 5.300000e+01 21 I would like to know what ever the data I've obtained is the number of hydrophobic interaction between the ligand and protein or I am wrong somewhere. Please help me. Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/g-mindist-reg-tp5000756.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
