[gmx-users] what means of contact in mindist?

范聪 fanc232 at nenu.edu.cn
Tue Feb 2 03:09:30 CET 2016

Hello, I'm very intreresting in this question, so can I join in ?
First, I wonder if there is "interactions" between hydrophbic residues. what I know is that for those nonpolar residues, their interactions with water is weaker than the polar attractions between two water molecules, so that water molecules gather and the nonpolar molecule is "squeezed out". That is why nonpolar residues gather and seem "interacting" with each other, am I right?
Second, I saw a question a few days ago which is similar to your quesion. The title is
How to get an index file containing non polar atoms in gromacs?published around 2015/01/24. I think you can have a check.
 Third, I think not only g_dist but also g_sas can help. Further more, PLATNUM may help, too. The "touching" surface of the hydrophobic parts of the ligand and the receptor can be evaluated by PLATNUM.

At 2016-02-01 21:56:24, masoud keramati <keramati.ma3oud at gmail.com> wrote:
>i mean interactions between hydrophobic residues in a protein-ligand

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