Dear all,
I have to analyze the trajectory and calculate all distances between a group of atoms (each separate particle) and all the surrounding waters, which were at the distance cutoff < 0.35. There were times, when I used gmx dist to calculate 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 number and then it was added into the index file. Final pdb for visualization consisted of the binding site and the water molecules bound to any HB-forming atoms 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 introduced 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!
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