PDB editing biopython

Question

[sajidiqbalpml]

Hi folks, I have amber topology and coord files and I use them in python. I want to collect water molecules using residue (wat) criteria under one variable as

water_mols = box1_mols.residue(wat)

Here, box1_mols contains all the molecules (protein + ions + water). and I want to assign individual parameters to each component. Any suggestion? Thanks

[Peter]

If this is a public dataset, giving the PDB identifier might make it easier for people to give precise answers.

You mention Biopython in the title, have you read or looked at the tutorial chapter on the PDB module? http://biopython.org/DIST/docs/tutorial/Tutorial.html http://biopython.org/DIST/docs/tutorial/Tutorial.pdf

[sajidiqbalpml]

yes, I can access to residues within molecule but want to extract whole molecules like water. I will recheck and see if it works. thank you