GROMACS version: 2022
GROMACS modification: No
Dear all,
I have to analyze the trajectory and calculate all distances between a group of atoms (each separate one) and all the surrounding waters, which were at the distance cutoff < 0.35. There were times, when I used gmx dist to calculate this and the output contained columns for the time step, distance, atom number of the protein, atom number of the water molecule number… If the count for the molecule was higher than, for example, 10 (covering a 500 ps period) we took the water molecule id into the index file. Final pdb for visualization consisted of the binding site atoms and the water molecules bound to any HB-forming atoms of the binding site at different periods of the trajectory. From these we concluded whether the part of the binding site could be occupied with water or not and it could be also implemented into the docking model development process…
For now, there are many different commands for distance evaluation, but which cooperation I should use (separate command doesn’t give the all data, while the most useful is pairdist now) to get the info - ps, protein atomid/resname, water atomid/resnumber, distance…?
Thank You!