How can I calculate RMSD between two ligands (crystal and docked)?
How can I calculate the RMSD value between crystal and docked structure of ligand using pyrx or VMD? Is it possible to calculate RMSD using pymol between the two ligands (crystal and docked)?
Hi Vijay,
The following VMD tutorial should help you:
http://chembytes.wdfiles.com/local--files/vmd/vmd-basic_tutorial-1_0.pdf
In using Pymol, LigAlign may be nice:
https://pymolwiki.org/index.php/LigAlign
And the following links may help you for RMSD calculation:
http://www.math.unm.edu/~vageli/codes/codes.html
https://github.com/charnley/rmsd
http://chembytes.wdfiles.com/local--files/vmd/vmd-basic_tutorial-1_0.pdf
http://translate.google.co.jp/translate?sl=ja&tl=en&u=http%3A%2F%2Fwww.cuemol.org%2Fja%2Findex.php%3Fcuemol2%2FMolSuperpose
Hi Vijay,
Yes possible with VMD. First, add the non-polar hydrogens to your PDBQT file then use VMD to align the crystallographic complex structure to your docked complex structure and calculate the RMSD. But RMSD Visualizer Tool -plugin is an extension for VMD is powerful. Its main functions include aligning molecules and calculating and visualizing RMSD (Root Mean Square Deviation) and RMSF (Root Means Square Fluctuation) data through trajectories.
I suggest Discovery Studio. Discovery Studio has easiest way to calculate RMSD between two ligands or proteins. To calculate RMSD between two small molecules the steps are
Load reference molecule >> structure>> RMSD>> set reference.
Then drag docked molecule to the same window>> select it >> structure>> RMSD>> all atoms or heavy atoms.
The RMSD will be shown to the Right side window.
Hossein Aghazadeh Thanks a lot for your response. Do you have some reference procedure for Discovery studio, If yes then please do share
Try chimera or fconv (command line) maybe:
https://www.cgl.ucsf.edu/chimera/
https://academic.oup.com/bioinformatics/article/27/7/1021/232039
http://pc1664.pharmazie.uni-marburg.de/drugscore/fconv_download.php
Vijay Nimbarte
Yes,
accelrys.com/products/datasheets/viz_in_ds17.pdf
Hope this helps.
Please check out the attached link:
https://www.researchgate.net/post/How_can_I_calculate_RMSD_between_two_ligands_crystal_and_docked
Please anyone tell me which molecule I will insert it ( out.pdbqt file or which) for both crystal and docked
and which software i can use to do this
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