Activity for rDock
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IZAZ MONIR KAMAL created ticket #15
Is it possible to run rDock from PHP-based-webserver through a python script ?
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sam created ticket #14
sdsort, sdreport and sdfilter problem
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improving the accuracy- optimizing the docking parameters
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Hi Sergi, I am using rdock for docking RNA-ligand, but with my HTVS ligand file, I am getting a Segmentation fault (I have splitted my files so split1.sd is one of them). I am not sure what is wrong with my input files and I would appreciate I you help me with it. I also used the DUD (ace) test files for my ligand database but still I am getting the same error. I appreciate it if you help me with this. I am using these command : rbcavity -r rdock.prm -d -was > cavity.log rbdock -r rdock.prm -p dock.prm...
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Sergio Ruiz posted a comment on ticket #12
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...
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Hi sergio, Thank you very much for your reply. You actually pointed out thr prolem. By visualizing I noticed my ligand is not defined in the vicinity of the receptor. How should I put the ligand in the vicinity of receptor? or what software or method I should use to define that? rbcavity -was -d -r <prmfile> will only creat a box around the ligand. Please help me with that so I can proceed with my simulation. </prmfile> Thanks a lot in advance. Bests, Sam
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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....
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Hi Sergi, Thank you for your reply. I defined the cavity. I have attached the outputs of running these commands: rbcavity -r rdock.prm -was > rna_cavity.log rbdock -r rdock.prm -p dock.prm -n 100 -i ligand.sd -o rna_docking_out > rna_docking_out.log sdsort -n -f'SCORE' rna_docking_out.sd > 2qwy_docking_out_sorted.sd sdrmsd ligand.sd 2qwy_docking_out_sorted.sd But still getting the same results. I can tell after running rbcavity commands the caviy has been determinded in the log file. Please let me...
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Sergi Ruiz posted a comment on ticket #12
Hi Sam, For what you explain, it looks like you wrongly defined the cavity. The sd file you use for defining it should be placed in the binding site, or you can define the cavity based on a set of coordinates. You can take a look at the cavity to confirm that: you can see how to do it here http://rdock.sourceforge.net/docking-in-3-steps/ (section 2). We cant help with just the prm file, but please take a look and let me know! Cheers, Sergio On Sat, 27 Jun 2020, 05:13 sam, sabm@users.sourceforge.net...
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I was wondering if anybody can hep me with this problem??
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no interaction with ligand and mol2
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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
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Anonymous posted a comment on ticket #11
Hello, I tried to install rxDock on Ubuntu 19.10, but I have problem on make linux-g++-64. Can I use this patch to solve the problem and how to use it? Many thanks! --Kaibo
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Tomasz Żok created ticket #11
A patch to allow compilation on newer systems
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Grigorii posted a comment on ticket #10
Ticket should be called "Project Support", sorry. Made a typo.
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Project Suppoer
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Scott Bembenek created ticket #9
Grid Scoring Option
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Hi Peter, yes I did set all the variables correctly, but it was never able to find the needed library. Anyway, I did successfully install it from the dockerimage. thanks for you help! Scott On Sat, May 4, 2019 at 3:34 AM Peter Schmidtke pschmidtke@users.sourceforge.net wrote: Hi Scott, Rather than going through the sometimes painful installation process did you check out a suitable dockerimage first? Informaticsmatters/rdock is one I often use and suits most use cases. On dockerhub they also provide...
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Peter Schmidtke posted a comment on ticket #8
Hi Scott, Rather than going through the sometimes painful installation process did you check out a suitable dockerimage first? Informaticsmatters/rdock is one I often use and suits most use cases. On dockerhub they also provide a dockerfile with all installation steps. As for your original question, did you define the rbroot environment variable? Did you source them correctly? Can you paste an example of your current LD_library path variable? Cheers Peter Sent from BlueMail On May 4, 2019, 12:05,...
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Problems with install under Centos7
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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
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Anonymous posted a comment on ticket #7
Hi. I recently joined the SourceForge communityy as I want to install rDOCK for my project. I also had aa "make linux-g++-64" error. I have attached the error code. I have XUbuntu Linux. To try and correct the error, I downloaded popt into my Downloads directory. This is where the rDOCK folder is downloaderd and unzipped. I navigated to the build folder and followed the instructions to install. I get the same same error. DO i need to install additional dependencies? If so, where should they be saved...
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Error while running "make linux-g++-64" inside build folder
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Anonymous posted a comment on ticket #7
Hi Sergio Thanks for your help. I finally decided to freshly install Ubuntu 16.04, which supports CUDA as well as rDock. The reason for not continuing with Ubuntu 18.04 was that I feared that downgrading the gcc version (to support rDock) might adversely affect other programs. Thanks once again. Munesh
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rDock Program hangs
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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...
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Munesh Singh Chauhan posted a comment on ticket #7
Hi Sergio I am not familiar with conda installation. Can you please outline step by step process of installing rDock using conda. I am facing the following errors. Though I must say that I tried several times with the conda isntall command. **munesh@munesh-Lenovo-ideapad-130-15IKB:~/rDock_2013.1_src/dev/build$ conda install -c bioconda rdock Solving environment: failed UnsatisfiableError: The following specifications were found to be in conflict: - rdock Use "conda info <package>" to see the dependencies...
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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...
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I am attaching the error log, while building on Ubuntu 18.04 using the following command: make linux-g++-64
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Hi Sergio, Many thanks for your prompt reply. I am looking to accelerate some features of rDock that are too slow using GPUs. So could you please suggest if possible portions of the rDock code (C++ functions) that are too slow and could benefit from multithreaded computing (I will be using CUDA to accelerate things). Unfortunately, I am not able to intall rDock using conda. Just curious to know if any one tried compiling rDock on Ubuntu 18.04 using "make linux-g++-64" that is without using conda?...
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Hi Munesh, Thanks for reaching us and using rdock. I have not seen this error in ubuntu 18.04. Good that you were able to install it in 16.04, but in case you need it in 18.04, please try to install it through bioconda repository using conda: conda install -c bioconda rdock Cheers! Sergio On Mon, 18 Mar 2019 at 06:59, Munesh Singh Chauhan munesh@users.sourceforge.net wrote: It seems the problem is with some copatibility issues in Ubunut 18.04. I am able to install and test properly in Ubuntu 16.04...
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It seems the problem is with some copatibility issues in Ubunut 18.04. I am able to install and test properly in Ubuntu 16.04 version. But is there any wayaround to install on Ubuntu 18.04?
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It seems the problem is with some copatibility issues in Ubunut 18.04. I am able to install and test properly in Ubuntu 16.04 version.
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Error while running "make linux-g++-64" inside build folder
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hi monsuru, it is probably due to a long string in the name or a field of the ligand, which makes rdock hang. please check fields longer than 32 characters and remove them. Also change the name of the ligand to something shorter. let me know it that worked your issue please. sergio
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Monsuru Mustapha created ticket #6
rDock Program hangs
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initial commit
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Installation Error
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Hi Rajiv, The error comes from not installing one of the dependencies (cppunit and...
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RJ posted a comment on ticket #4
Dear Sergio, I am also did not find any error on compiling but "make test" produces...
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Hi Sergio, The binary file works fine for docking. How one can dock the list of ligands...
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Hi Rajiv, I've checked your attached file and I didn't find any error... are you...
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Anonymous posted a comment on ticket #3
Great! Thanks Sergio. ciao, Ant
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Installation Error
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Anonymous modified a comment on ticket #3
Ant
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Usage:Segmentation fault !?
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If the compilation tests succeded and the running tests were correct, rdock is able...
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Hi Ant, Ligands and decoys txt files can be downloaded in the beggining of the tutorial....
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Anonymous posted a comment on ticket #3
Hi Sergio, I'm trying to use your DUD list and tutorial to make the ROC curve highlighted...
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Anonymous posted a comment on ticket #3
Ant = chubbant - at - gmail.com
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ProzacR posted a comment on ticket #2
did the compilation tests succeed? Yes have you correctly declared the needed variables?...
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Tutorials Docking in 3 steps do not explain <ligand>.sd
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Please use the tickets properly: this information is easily available in internet...
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without providing more details it's difficult to know exactly what's happening......
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Tutorials Docking in 3 steps do not explain dock.prm
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Hi, dock.prm is thoroughly detailed in the manual (pages 14, 18 and surrounding)...
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Tutorials Docking in 3 steps do not explain <ligand>.sd
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Usage:Segmentation fault !?
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Tutorials Docking in 3 steps do not explain dock.prm
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changed ht_protocol_finder.pl to rbhtfinder, as...
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changed src/exe/rbdock.cxx: an if statement has...
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Fixed csh dependencies: removed buildnum.csh, r...
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rDock released /README
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Cleaned up not necessary files. Removed rodck_n...
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Daniel Álvarez committed [r20]
sdrmsd fixed output sdf with molecules in same ...
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fixed sdmodify to print out help message
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Modified sdrmsd to allow pose filtering by RMSD...
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Removed "using namespace std;" from src/GP/RbtG...
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fixed headers from src/gp/ folder
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Added error checking in sdtether and sdrmsd
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