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I need to calculate the RMSD between a co-crystallized ligand and my ligands and a non-co-crystallized ligand with GLIDE but I don't know how. Could someone explain to me how to do it? Many thanks in advance.

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    $\begingroup$ Is using Glide necessary in your project? So many softwares can calculate RMSD, I name a few of them: VMD, GROMACS, MDanalysis, Chimera... $\endgroup$
    – Y. Zhai
    Commented Aug 24, 2020 at 11:44
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    $\begingroup$ +1. Hopefully you get an answer quickly. Maybe one of the programs that Y. Zhai has recommended could help you, but if you do need to use Glide for some reason, I hope someone here can help yo quickly. $\endgroup$ Commented Aug 24, 2020 at 17:42

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The software GLIDE is not used for RMSD calculation. GLIDE is dedicated to do small ligand/protein docking (rigid/rigid and flexible/rigid).

You can calculate the RMSD by hand, using MAESTRO, CHIMERA and VMD interfaces (all free for academics) among many other software (also free).

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  • $\begingroup$ Thank you i thought i hed to use the core tab of glide, but can you explain me how ? because I have to do this but nobody tell me how and the deadline of my thesis is very close :( $\endgroup$
    – Giu
    Commented Aug 25, 2020 at 9:04
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    $\begingroup$ If you are using MAESTRO, just load both structures you want to determine the RMSD, go to the TASK menu/icon, search for SUPERPOSITION and setup the calculation (you have to put the structures at workspace or select both in the table). $\endgroup$
    – Camps
    Commented Aug 25, 2020 at 18:21
  • $\begingroup$ Many thanks :) It's the same for the receptor with no non-co-crystallized ligand? beacause i work with 2 receptor one of ths have a non-co-crystallized ligand instead in the otheor one i work in a allosteric binding site with no non-co-crystallized ligand but i have to compare data with a reference ligand known in litterature. $\endgroup$
    – Giu
    Commented Aug 27, 2020 at 9:49
  • $\begingroup$ Sure. The calculation of the RMSD is made in the same way. $\endgroup$
    – Camps
    Commented Aug 27, 2020 at 10:43
  • $\begingroup$ thank you so much. $\endgroup$
    – Giu
    Commented Aug 27, 2020 at 14:19

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