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remove_waters_and_ions

This is an old revision of the document!


Remove water and ions from trajs

Open a ptraj.in and add the following lines:

trajin rec.all.mdcrd
strip :WAT,Na+,Cl-
trajout rec.mdnw.mdcrd

Now enter ptraj rec.top < ptraj.in

But if you need some waters around your ligand or QMMM region? No problem! Forget 'strip' and add these lines to your ptraj.in:

solvent byres :WAT
closestwater 20 :464 first (WAT around residue 464 until 20 A of distance will be preserved)

remove_waters_and_ions.1457360540.txt.gz · Last modified: 2016/03/07 14:22 by root