I am trying to extract the coordinates of solvent molecule from a peptide PDB, within a distance of 3 ang of O and N atoms in peptide. Using VMD, I can extract up to 3 ang of peptide. I want to calculate distance from atoms. I am trying to use neighbor search module but I don't know how I should proceed with atoms?
I could create a list of N and O atoms from peptide and calculate distance between peptide atoms and water.
Is there any alternate method?