Sergio Ruiz

Hi Sam, That's correct, glad you fount it out! It's up to you to choose a method to define the cavity, but I would recommend pocket ( https://github.com/Discngine/fpocket) and then using the desired pocket identified as a dummy ligand for rdock cavity definition. Note also that you can use the "Two sphere method" to define the cavity (section 5.1 in the documentation http://rdock.sourceforge.net/wp-content/uploads/2015/08/rDock_User_Guide.pdf), where you would only need the coordinates of the region...

Hi Sam, The program is working fine. As I mentioned in the previously, please follow the instructions on section 2 of http://rdock.sourceforge.net/docking-in-3-steps/: If you run rbcavity with the -d option: rbcavity -was -d -r <prmfile></prmfile>, it will create a grd file that you can open in pymol and will help you troubleshoot your problem. The ligand you are using to define the docking site is not in contact with the receptor, so all the docked poses will not interact with the receptor, either....

Hi all, Thanks a lot Thomas for your patch. We are considering porting everything to github and will include your patch when we do it. @Kaibo, yes, feel free to use it as Thomas suggested. In case it doesn't work, you can try with conda or, as previously mentioned, the dockerhub container by 'informatics matters' works good: https://hub.docker.com/r/informaticsmatters/rdock/ Cheers, Sergio

Hi, All the dependencies are detailed in the manual and the installation webpages. Based on the error log that you attached, looks like you dont have popt and popt-devel installed (or correctly pointed). Please check that and rerun rdock installation. You can also try installation with conda, which already manages all dependencies: conda install -c bioconda rdock Thanks, Sergio

Error while running "make linux-g++-64" inside build folder

rDock Program hangs

Hi Munesh, It's a standard conda package installation, it will automatically download all dependencies and install them accordingly: $ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 18.04.1 LTS Release: 18.04 Codename: bionic $ conda create -n docking-rdock Collecting package metadata: done Solving environment: done Package Plan [...] To activate this environment, use $ conda activate docking-rdock To deactivate an active environment, use $ conda deactivate...

Hi Munesh, I think it is related with your compiler version. Ubuntu 18.04 comes with gcc 7.3 by default, so you need to install 4.8.0 or 5.4.0, which I have succeed installing with (i will update the manual). In any case, conda installation was straightforward with fresh Ubuntu 18.04, so I recommend you to try a bit more on that side, as all dependencies and older versions are well managed with the conda environment. Best, Sergio On Wed, 20 Mar 2019 at 15:01, Munesh Singh Chauhan munesh@users.sourceforge.net...