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calculate_rmsd_of_elements_of_the_simulation [2016/03/07 14:23] (current)
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 +====== Caculate RMSD ======
  
 +Let be your system a complex with a ligand named LIG.\\
 +Open a ''​ptraj.in''​ and add the following lines:\\
 +
 +''​trajin rec.all.mdcrd''​\\
 +''​reference rec.crd''​\\
 +''​center ~:​WAT,​Na+,​Cl-''​\\
 +''​image byres :​WAT,​Na+,​Cl-''​\\
 +''​rms reference mass out rmsREC @CA''​\\
 +''​rms reference mass out rmsLIG :LIG nofit''​\\
 +''​atomicfluct out flucREC ~:​WAT,​Na+,​Cl-,​LIG byres''​\\
 +''​rms reference mass out rmsLIGfit :​LIG''​\\
 +\\
 +Now enter ''​ptraj rec.top < ptraj.in''​ \\
 +\\
 +You should see three different files: ''​rmsREC''​ (RMSD of Cα atoms of the target), ''​rmsLIG''​ (RMSD of all atoms of the ligand), ''​flucREC''​ (RMSD fluctuations of the residues of the target)
calculate_rmsd_of_elements_of_the_simulation.txt · Last modified: 2016/03/07 14:23 by root