I need to measure the RMSD after I docked the ligand using GOLD 5.1 .
There are two interpretations of what I think you are wanting to do and both are possible in GOLD 5.1.
If you have a reference structure and you want to calculate the RMSD of the solutions to this reference structure you can do this as part of the docking protocol. You can specify the reference ligand model at the same time as you specify the ligand to be docked in the set-up.
If instead you want to calculate the RMSD's between different docking solutions from a single docking run this can be done with the analysis tool that comes (free) with GOLD 5.1, GoldMine. The relevant documentation can be found on pg 37 of the file below.
http://www.ccdc.cam.ac.uk/Lists/DocumentationList/goldmine.pdf
Good luck
John
Did the Gold program on your computer come along with a manual? I suggest you look up the command on the manual. Thanks
There is an online server called DSX (http://pc1664.pharmazie.uni-marburg.de/drugscore/introduction.php). Here you can upload your gold output file to calculate RMSD and additionally re-rank your poses and analyses poses on basis of Drug score potential/ paired potential. You should try this...
I think John is right
You need to add reference ligand to calculate the RMSD based on the cocrystal ligand or another reference ligand present in the actove site.
Regards
I also have the same problem in calculating RMSD after docking. I have already known how to calculate it during docking, but I am now trying to do it afterwards...
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