calculate_rmsd_of_elements_of_the_simulation
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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
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