Extracting coordinates of possibly H bonded solvent molecule using BioPython
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6 weeks ago
GS • 0

Hi,

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?

S

PDBParsing python Biopython Bioinformatics VMD • 78 views
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