• RE: Invalid scores when setting distance constraint from cofactor to substrate, ligand to be docked

    Ilenia,

    Thanks for the prompt reply. I verified that a rename fixed the issue unfortunately that was a ligand that I got from some other application's sample to avoid sending confidential data. I get the same problem when I use one of my ligands named B4C. I renamed the PHE ligand to B4C and it ran just fine but when I used the B4C ligand it went back to having the score issue (see below) which is really odd. I also used CCDC's SAH ligand and it did not have an issue.

    I figured there is some additional issues with CCDC handling the B4C mol2 file and after manually looking at the mol2 file contents, the issue turns out to be this one line:

    @<TRIPOS>SUBSTRUCTURE
    1 UNK 1 RESIDUE 1 _ UNK

    Once I changed UNK to B4C, everything works. Unfortunately, there are no errors or warnings from the API, and it only happens when I use the cofactor-ligand in the constraint which is why I assumed it was an issue with the update. Anyway, thanks for your help, it all seems to be working now. May want to add some warning in the log or add the UNK issue and solution in some reference document since it will probably save someone a significant amount of time.

    Thanks,

    Hector

    -----------------

    Fitness list for ligand file B4C.mol2, molecule 1

    Mol No Score S(PLP) S(hbond) S(cho) S(metal) DE(clash) DE(tors) DE(con) intcor time

    3 -3102.19 -44.58 1.64 0.00 0.00 0.00 0.63 -3150.44 0.00 0.031
    2 -3103.31 -42.46 1.88 0.00 0.00 0.00 0.49 -3150.44 0.00 0.047
    1 -3103.63 -42.14 1.70 0.00 0.00 0.00 0.22 -3150.44 0.00 0.000


    Average Values:

    -3103.04 -43.06 1.74 0.00 0.00 0.00 0.44 -3150.44 0.00 0.026

  • RE: Invalid scores when setting distance constraint from cofactor to substrate, ligand to be docked

    I sent structures and sample code to  support@ccdc.cam.ac.uk...

  • RE: Invalid scores when setting distance constraint from cofactor to substrate, ligand to be docked

    Illenia,

     

    I was out of the office for a couple of weeks and just got back today. I was hoping that it failed for you with the files you had used since the original files that I have the problems with are confidential and I cannot send them to you. I will try to make it fail using some files from PDB. This is not ideal for a lot of reasons but I guess I don't have too many other options.

    Hector

  • Invalid scores when setting distance constraint from cofactor to substrate, ligand to be docked

    Late last year, I reported a problem with the CSD API when setting constraints between the protein file atoms (which include a cofactor) and the ligand (to be docked) atoms which is loaded as a separate molecule. After you guys were able to duplicate the problem, it was reported to be fixed.

       see "distance constraint from fixed cofactor to substrate (ligand to be docked)" in the Discovery section of the forum, Nov 26, 2018.

    I got side tracked with another project and now I'm back on the original project where I found the issue. The good news is that I can now set a distance constraint between the cofactor (included with the protein molecule) and the ligand (a separate molecule). The bad news is that even though it runs, the scores are all messed up as a result of the DE(con) having a value of -1777.79 for all poses:

      debug msg:

          Distance constraint from cofactor H, Coords(x=13.385, y=10.697, z=11.012), to ligand C, Coords(x=-8.597, y=3.842, z=0.108), range 2.0 to 5.0

      rank file output data (a couple of rows):

      Mol No Score S(PLP) S(hbond) S(cho) S(metal) DE(clash) DE(tors) DE(con) intcor time

      4 -1728.75 -50.21 0.00 0.00 0.00 0.00 0.58 -1777.79 0.00 0.812
      1 -1728.86 -47.31 0.99 0.00 0.00 0.00 0.68 -1777.79 0.00 0.000

    The coordinates shown in the debug message are the original ones when the protein and ligand files are loaded. I printed them to make sure the right atoms were being passed to the constraint, and they are.

    Everything works fine when the constraint is not set or all atoms in the constraint are in the protein file. You were able to duplicate the original problem, see original forum entry listed earlier, so hopefully you can use a similar approach to duplicate the scoring issue. BTW, setting a constraint from a protein residue atom to the ligand also has the same issue. I'm using Python API 2019 (same computer info as previous issue). Let me know if you need any additional information.

    Thanks,

    Hector

  • RE: Installation issue with Qt xcb

    Dave,

    Thanks for the information. Unfortunately the end result was still the same. I manage to find a couple of problems, and get around them, so I will post them here in case someone else runs into this issue:

    1. When I ran the command ldd on libqxcb.so ($PYTHONHOME/lib/python2.7/site-packages/ccdc/_lib/plugins/platforms) I found:

    libSM.so.6 => not found
    libICE.so.6 => not found

    Running "sudo apt install libsm6" solved both dependencies

    2. Once that was done then I got the following message when trying to import ccdc in python:

    Python 2.7.15 |Anaconda, Inc.| (default, Dec 14 2018, 19:04:19)
    [GCC 7.3.0] on linux2
    Type "help", "copyright", "credits" or "license" for more information.
    >>> import ccdc
    QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-<userid>'
    qt.qpa.screen: QXcbConnection: Could not connect to display
    Could not connect to any X display.

    SInce I only want to run the CSD API without any display, I solved it by adding:

    export QT_QPA_PLATFORM='offscreen'

    to ~/.bashrc (https://github.com/ipython/ipython/issues/10627)

    Turning off the Qt display was one of my original questions and this is one way to do it. I'm not sure if there will be any issues going forward but I was able to run my existing docking code that was working with the CCDC 2018 version without any issues.

     

    Thanks for your help,

    Hector

     

  • Installation issue with Qt xcb

    I have successfully installed the linux version of CCDC 2019, with the Python API, on the Ubuntu terminal, 16.04.3 LTS (Xenial Xerus), of a Windows 10 system. Unfortunately, when I try importing the ccdc module:

    ./run_csd_python_api

    Python 2.7.15 |Anaconda, Inc.| (default, Dec 14 2018, 19:04:19)
    [GCC 7.3.0] on linux2
    Type "help", "copyright", "credits" or "license" for more information.
    >>> import ccdc
    This application failed to start because it could not find or load the Qt platform plugin "xcb" in "".

    Available platform plugins are: xcb, eglfs, minimal, minimalegl, offscreen, vnc.

    Reinstalling the application may fix this problem.
    ./run_csd_python_api: line 4: 2116 Aborted (core dumped) python

    ***************

    The ccdc library is the only one defined in the library path

    echo $LD_LIBRARY_PATH
    /home/<userid>/CCDC/Python_API_2019/miniconda/lib/python2.7/site-packages/ccdc/_lib

    and the ccdc bin is properly set in the $PATH.

    *******

    It seems to me that there should not even be a reason for trying to load the Qt plugin at all since this is a terminal only with no need for X11 support for GUI display (I only need to run the API). Is there a way to disable it (e.g.set to TKagg or agg) or is there some way to get around this issue?

    Thanks,

    Hector

  • RE: Is it possible (license) to run our CSD API server on Google cloud?

    Ilenia,

    Perfect. Thanks,

    Hector

  • Is it possible (license) to run our CSD API server on Google cloud?

    Hi,

    We are exploring the options of using Google cloud services and would like to find out if it is possible to setup our server running the CSD API on the cloud (to run on a need to basis with variable amount of resources as needed) - is that allowed by the current licensing? Any relevant information will be helpful.

    Thanks,

    Hector

  • RE: distance constraint from fixed cofactor to substrate (ligand to be docked)

    Ilenia,

    Thanks for the update. I went to download it and try it out but I noticed it requires a 2019 license which we have not gotten yet so it will have to wait (we have the 2018 license and are in the final stage of evaluating multiple tools to decide which ones to keep/get next year). We will be making a decision soon.

    Thanks for all your help,

    Hector

  • RE: distance constraint from fixed cofactor to substrate (ligand to be docked)

    That will be helpful, Thanks...