Which tools for calculation of number of nonpolar contacts?

User discussions
1

Hi gmx users,

With what command from Gromacs software can the parameter of Fig 1E (number of nonpolar contacts) of the following article be obtained?

Or the parameter of Fig 8 of the following paper (Occupancy of hydrophobic interaction in protein-ligand complex)

Biomolecules | Free Full-Text | Structural Basis for Vascular Endothelial Growth Factor Receptor Activation and Implications for Disease Therapy | HTML)?

Please guide me.

2

Hi,
I do not know in your specific case, but gmx mindist output the number of contact between one group and a number of other groups.
Best regards
Alessandra

3

Hi. Thanks Alessandra.

I used this command: gmx mindist -f md.xtc -s md.tpr -n index.ndx -d 0.6 -group

And I selected two groups. But I obtained only 1 output file (mindist.xvg) containing distance info and without info about number of contacts.

In the online manual, I saw:
gmx mindist computes the distance between one group and a number of other groups. Both the minimum distance (between any pair of atoms from the respective groups) and the number of contacts within a given distance are written to two separate output files.

How to resolve it?

4

You will need to use -on to get the output time series of contacts within your chosen groups.

5

Thanks Justin.
My problem was solved. Now, I have another question:

Based on manual, default distance for contacts is 0.6. Is this distance appropriate for evaluation of number of non-polar contact? Or should I choose another amount for -d ?

6

I think the default value comes from an approximation of the sum of van der Waals radii for generic atom types. You’d have to determine if such a value is reasonable, and I have no real insight as to whether it is, though I suspect it is fairly widely used.

7

Hello, I am trying to calculate the contacts of hydrophobic interactions. To do so, I selected the sidechains of the hydrophobic residues and created an index file for that. After that by using the following command, I calculated the contacts:
gmx mindist -f rep.trr -s protein.pdb -n hydrophobicresidues.ndx -d 0.45 -group yes -od -on

However, in the numcont.xvg, it calculated the same contact value for each frame. It seems to bit strange to me. How can I support my results?