User Tools

Site Tools


remove_keep_specified_waters_and_ions

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

remove_keep_specified_waters_and_ions [2016/12/16 07:15] (current)
root created
Line 1: Line 1:
 +====== Remove/Keep (specified) waters 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 do you need some waters around your ligand or QMMM region (highly advisable)? No problem! Forget '​strip'​ and add these lines to your ptraj.in:\\
 +\\
 +''​solvent byres :​WAT''​\\
 +''​closestwater 20 :464 first **(Up to 20 WAT molecules around residue 464 will be preserved)**''​\\
remove_keep_specified_waters_and_ions.txt ยท Last modified: 2016/12/16 07:15 by root