[gmx-users] distance between protein and ligand

Archana Sonawani ask.archana at gmail.com
Tue Oct 9 06:48:16 CEST 2012


I have simulated a protein-ligand complex for 5ns. I checked distance
between the important residues of protein and the ligand using g_dist. My
question is can the distance between the two groups decrease  from the
initial distance (docked complex as starting structure for simulation). I
know it may increase or may remain same at the end of the simulation.

for example: starting distance is 0.77nm and final distance is 0.8nm but
the intermediate course of simulation (around 3ns) it has decreased upto
0.65. The complex shows stability after 2ns. While the SASA between the two
groups is around 6.3 nm2  throughout the simulation which is very high.

This is very contradicting result. Is something wrong in the simulation?

Thanks in advance.

Archana Sonawani-Jagtap
Junior Research Fellow,
Biomedical Informatics Centre,
Mumbai, India.

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