[gmx-users] g_mindist

ahmet yıldırım ahmedo047 at gmail.com
Sat Jul 2 23:18:04 CEST 2011

Dear Justin,

You said before "you can obtain some idea by using g_mindist to calculate
hydrophobic and hydrophilic contacts between the protein and ligand".

That is, I can explore whether there is hydrophobic or hydrophilic feature
of ligand using g_mindist tool. is this correct?
I did the calculations related to protein_ligand interactions (protein
contains two ligand). I plotted the graphs of distance and numcount versus
simulation time for each ligand. The number of contacts in  ligand x is more
than the other ligand y. Which of this ligands are hydrophobic? Which is
hydrophilic? I know you are not private tutor. Please don't be angry :(

Thanks in advance
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