PyRx - Virtual Screening Tool Activity
Virtual Screening software for Computational Drug Discovery
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sarkiss
Activity for PyRx - Virtual Screening Tool
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Broto Santoso posted a comment on discussion General Discussion
Hi Sarkis I loved to get the coupon too, would you like to give the information to our institution, andi.suhendi(at)ums.ac.id is head of pharmacy program in our institution. Thank you. Best regards, B Santoso
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Sarkis Dallakian posted a comment on discussion General Discussion
Please undo it and use the same logic you used to set the workspace to C:\pyrx_dir\latihan01 and set it to the same with added _workspace. You can also change the workspace by editing the PyRx_workspace/preferences.ini in your home folder.
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faizah fulyani posted a comment on discussion General Discussion
Hi Sarkiss, i did, and now the pyrx wont start at all it gave the following error [image: image.png] On Wed, Jul 16, 2025 at 10:08 PM Sarkis Dallakian sarkiss@users.sourceforge.net wrote: Replace C:\pyrx_dir\latihan01 with C:\pyrx_dir\latihan01_workspace error with pyrx 1.1_error local variable 'targetName' referenced before assignment https://sourceforge.net/p/pyrx/discussion/general/thread/19e2d845fc/?limit=25#c324/fc1c Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/pyrx/discussion/general/...
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now this error appear and it wont start at all Traceback (most recent call last): File "C:\Program Files\PyRx\1.1\runPyRx.py", line 89, in <module> startPyRx() File "C:\Program Files\PyRx\1.1\runPyRx.py", line 38, in startPyRx frame = MainFrame(None, -1, size=(width, height-200)) File "C:\Program Files\PyRx\1.1\lib\site-packages\PyRx\wxMainFrame.py", line 167, in init self.autodockNav = AutoDockNavigator(self) # Navigator -> AutoDock tab File "C:\Program Files\PyRx\1.1\lib\site-packages\PyRx\autodockNavigator.py",...
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PrRx won't open
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Replace C:\pyrx_dir\latihan01 with C:\pyrx_dir\latihan01_workspace
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hi everyone, i am new to pyrx and everytime i run vina, i got this log error. what step that i missed here? ERROR|2025-07-16 14:18:27,039|Open C:\pyrx_dir\latihan01\Macromolecules\1bdg_receptor\39562_uff_e=345.55_out.pdbqt for details. local variable 'targetName' referenced before assignment
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Hi Sargis, i bought version 1.1 end of last year, i also want to try the new feature of 1.2 . can i get the coupon as well. thank you
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Martin KIENDREBEOGO posted a comment on discussion General Discussion
PyRx 0.8 Autodock Wizard cannot run to the end!
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Dear Sir, my my autodockwizard system can't find or open ligan folder. I tried unsuccefully by renamin ligand with short name. Pyrx 0.8 Window 11 Familly, version 24H2
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姜小白 posted a comment on discussion General Discussion
The incorrect description is Error in : <bound method="" runautogrid.tryrun="" of="" \<pyrx.autogridpage.runautogrid;="" proxy="" \<swig="" object="" type="" 'wxpanel="" *'="" at="" 0xab684b0=""> >> Python 2.6.5 (r265:79096, Mar 19 2010, 21:48:26) [MSC v.1500 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information.</bound>
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Hi Stephen, Yes, you need to restart PyRx for it to pick up the new workspace. It is better to use multiple workspaces rather than one big one for performance.
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Stephen Haines posted a comment on discussion General Discussion
Hi Sarkis Just a follow up question. If I have two workspace folders called PyRx_workspace_project1 and PyRx_workspace_project2, can I switch between them by editing the PyRx preferences and choosing the appropriate folder for the AutoDock workspace, and still avoid the logging error? Thanks Stephen
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Omar Attraqchi committed [r529] on Code
Update Dockamon Path For New Dockamon Version.
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Thanks, that worked. Cheers Stephen
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Include SMINA box only if the smina path exists
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Fix for https://sourceforge.net/p/pyrx/discussion/general/thread/d5fcde628e/?limit=25#9c26
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Hi Stephen, It seems to happen because D:\Docking\PyRx doesn't include 'workspace'. You can fix it by replacing D:\Docking\PyRx with D:\Docking\PyRx_workspace, for instance. I'll look into fixing this in the next release. Thanks, Sargis
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Hi Stephen, The new version requires an executable that can't be included with updates. I'll PM you a coupon code. Thanks, Sargis
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Hi Sargis When I check for updates in PyRx 1.1 it tells me there are no new updates available, but I see in your blog that 1.2 has been released. Will that be made available via the update check process in version 1.1? Regards Stephen
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Hi Sargis The following error message occurs in the PyRx logger window for every docking run I perform with Vina. It doesn't seem to affect docking, but it would be nice for it to be fixed so PyRx doesn't switch to the logger tab after each run. ERROR|2025-06-11 13:08:55,207|Open D:\Docking\PyRx\Macromolecules\3ksc_prolegumin_abc_chains\quercetin_3-d-glucoside_uff_e=608.66_out.pdbqt for details. local variable 'targetName' referenced before assignment Regards Stephen
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Checking SMINA Is Available To Be Included As An Option For Docking Software.
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Updating SMINA Path.
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Adding SMINA As Docking Software Option.
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Correct Temporary File Creation Path To Avoid Permission Issues.
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Changelog
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Changelog
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Changelog
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Changelog
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Changelog
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1,2
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Adding AlphaFold Database Structure Fetching Functionality.
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Add a hide button to the Binding Sites Panel for hiding displayed binding sites.
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Adding Binding Sites Detection & Panel. Updating MolDetsPanel With Charge Visualization.
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If you know a little Python, you can modify the code to set Num modes for Vina: https://sourceforge.net/p/pyrx/discussion/general/thread/b70524ed/
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Akanksha posted a comment on discussion General Discussion
Is this option available in the free version?
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Dear Sir, Thank you for the message. For 1, I would need the specs of your computer, the size of the protein and ligand, and the search space. My guess is that the search space is too large. I recommend making the search space smaller, otherwise,, it would take a long time for Vina to run. For 2) I need steps to reproduce it. In other words how did you get that error? 3) is a warning message that can be ignored.
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abdul azeez sayed posted a comment on discussion General Discussion
Dear Sir, we purchased PyRx software for academic purposes, i am getting this error message attached in this email for your reference. insufficent memory Order ID: PYR241121-4896-32101 PyRx 1.1
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The current version only supports python 2. I don't know what's causing this. I'm happy to help with any issues that happen with the paid version.
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Sukaina Abbas created ticket #93
Runtime Std error This application has requested the Runtime to terminate it in an unusual way
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Muzammil Kabier posted a comment on discussion General Discussion
Most probably the binding site you have chosen is wrong , if RMSD is this much . Are you talking about Redocking? Please mention the procedure you have followed
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You can get the 64-bit version. I'll give a full refund, if it doesn't solve this issue .
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Bhrundha K posted a comment on discussion General Discussion
Thank you very much for your prompt response. I request you kindly permit us to avail a trial version of the 64-bit version, so that we will get to know if it works to give our intended output. At this point of time, I have no option to pay the amount for the paid version as we have very limited funding for academic research. I am standing at a roadblock in my research because of this issue. Could you please help me with this on a humanitarian concern? It is great to have extended support like this...
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Assuming that your computer has sufficient memory this can be solved buy getting the paid version. The free version is 32-bit while the paid version is 64-bit. I'm also happy to fix any issues you encounter with the paid version.
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Dear Sir I am Bhrundha, a Ph.D. scholar from Kerala Agricultural University, Kerala, India. I am currently conducting research on small molecules and entering into the use of PYRX software (free version) for my work. It is great that we have an accessible free version of PyRx, for students like us who cannot afford even the Academic Version. Thank to your Team. I have done dummy docking assays to get used with the software, even with a batch of molecules of 25. However, I have been encountering an...
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Walter Kambasiya posted a comment on discussion General Discussion
Hello sir. My latest version of PyRx is giving me high RMSD values above 100. I am a bit concerned if they are using AngStrom. Your response is greatly appreciated
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Yes, in the latest version, there is an option to set Num modes for Vina https://sourceforge.net/p/pyrx/discussion/general/thread/cef07fd6ea/
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Is there a way to increase number of docking poses in PyRx to 100?
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Please get the latest version and let me know if this error remains. You could have started with thanking me for the free version, but no you want more. What are you expecting with the free version?
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Please get the latest version and let me know if this error is still there,
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Please get the latest version an let me know if this error is still there,
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Niharika D Kulkarni created ticket #92
Parse line error
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You can also use this link for tax question https://fastspring.com/consumer-support-form/tax-vat-gst/ or this for questions related to https://fastspring.com/consumer-support-form/ to purchasing.
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@anchikam you just enter purchase order number in the checkout. If you do a purchase order through the site it would give you a link where you can make a payment.
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Anna Manukyan posted a comment on discussion General Discussion
@sarkiss I have the purchase order. What is the next step?
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@anchikam you are welcome. You can do Wire Transfer, Check or Money Order or Purchase Order.
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@sarkiss I have a purchase order ready. The grant I have doesn't have a credit card - it has to be done theough the budgeting. How can I proceed with the downloading in this case? Thanks again.
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Thank you @sarkiss
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Hi @anchikam , that link I provided list all the info needed plus has W-9. They can email b2b@fastspring.com for more info.
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Hi @sarkiss, my university's purchasing has asked for additional information to be able to register the vendor. "Purchasing will need a copy of vendor’s W-9 and name and email or person completing registration. Please note, the person needs to be able to access company’s financial information." Would you be able to provide it (email)? Thank you.
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Hi sure, you can get quotes for free from https://pyrx.sourceforge.io. Please let me know if you have any questions.
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Oscar Barba posted a comment on discussion General Discussion
Hi, I am trying to get a quote for a commercial license: can you please point me in the right direction? Thanks
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Hi Irene, I DM you a coupon code. MacOS version doesn't work on 64-bit Mac.
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Irene Zegar posted a comment on discussion General Discussion
Hi Sarkis, Her is my order number for the purchase that I made on 6/17/22: PYR220617-1785-97116. I am also attaching the invoice for the purchase. In addition , I wanted to know if you have a MacOS version of the software. Thank you
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Thank you! I will have to ask our secretary and will send it to you tomorrow morning.
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Hello, please dm me your order number and I can't send you a discount code.
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Hello, I am a professor of chemistry at Pittsburg State University. I purchaced PyRx around 2018. I have recently lost the computer that PyRx was loaded on. Is there away I can download another copy. The software was purchase through the Chemistry department at Pittsburg State University but using my research funds. Thank you in advance for your help
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@sarkiss Thank you so much!
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Hi @anchikam , you can use this document that has al the info needed for vendor on-boarding: https://fastspring.com/wp-content/uploads/2023/07/2024-FastSpring-Vendor-Onboarding-Fact-Sheet-CONFIDENTIAL-1-2.pdf
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Hi @sarkiss, I would also like to purchase the academic version but our institution requires a vendor to be registered with the institutional procurement service - CUNYBuy. They need W9, contact information and an address. Would you be able to provide this information? If you have any other suggestions, please let me know. Thank you, Anna.
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No, sorry, I don't have time, space, or energy for a 64 bit macintosh version. If I can find a co-founder who uses Mac maybe.
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Blake Peterson posted a comment on discussion General Discussion
Is there a possible release date for a 64 bit macintosh version?
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Changelog
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addin Omar Al-Attraqchi
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Dear Flavio, Sorry, I don't have bandwidth for this currently. I have Ubuntu 20.04 vm and don't have time to get a newer vm. Best regards
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Flavio Augusto Vicente Seixas posted a comment on discussion General Discussion
Dear Sarkis. I really appreciate your help. However, running PyRx in Windows is not an option for us, due to OS limitations. So, I try to install Ubuntu 24.10 64-bit, Kernel Linux 6.11.0-14-generic x86_64 replacing CentOS9. I successful install PyRx 0.9.2 in Ubuntu, but when I follow the instructions for update the version ( https://sourceforge.net/p/pyrx/code/HEAD/tree/PyRxDev/ ), I found the following error message: root@perseus:/usr/local/PyRx-0.9.2# ./run.sh root@perseus:/usr/local/PyRx-0.9.2#...
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Add "is_pose" argument to AddMolecule and GenerateAssambly functions in molNavigator.py to explicitly make docking poses generated as BallsAndSticks in GenerateAssambly even if the number of atoms > 200. This previously caused issue with ligands > 200 atoms being rendered as Lines when selected from VinaWizard. The VinaWizard in OnSelect passes is_pose as True to the mentioned molNavigator.py functions to always display ligands as BallsAndDSticks even when ligands have > 200 atoms.
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Dear Piyush, Thank you for your interest in purchasing PyRx. Unfortunately, lanthanum and similar elements are not supported by AutoDock/Vina and most forcefields, thus they cannot be processed. If you are interested, we can try to provide a custom approach, if you are only docking single elements (i.e. as in the ligand you provided), it might be possible to write a custom script to perform docking on the single elements, if you are interested in this service, please contact us via email (dallakyans@gmail.com...
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Dear Piyush, Thank you for your interest in purchasing PyRx. Unfortunately, lanthanum and similar elements are not supported by AutoDock/Vina and most forcefields, thus they cannot be processed. If you are interested, we can try to provide a custom approach, if you are only docking single elements (i.e. as in the ligand you provided), it might be possible to write a custom script to perform docking on the single elements, if you are interested in this service, please contact us via email (dallakyans@gmail.com...
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Piyush Kumar modified a comment on discussion General Discussion
Hello, I will buy the Pyrx 1.1 but i only have one question. I am unable to process lanthanum and rare earth elements as ligands in Pyrx 0.8 free version. Can you please confirm that you can do it in the latest version? Here's the ligand file: https://www.rcsb.org/ligand/LA
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Hello, I will buy the Pyrx 1.1 but i only have one question. I am unable to process lanthanum and rare earth elements as ligands in Pyrx 0.8 free version. Can you please confirm that you can do it in the latest version? Here's the ligand file: https://www.rcsb.org/ligand/LA
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Hello, I will buy the Pyrx 1.1 but i only have one question. I am unable to process lanthanum and rare earth elements as ligands in Pyrx 0.8 free version. Can you please confirm that you can do it in the latest version? Here's the ligand file: https://www.rcsb.org/ligand/LA
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I will buy the Pyrx 1.1 but i only have one question. I am unable to process lanthanum and rare earth elements as ligands in Pyrx 0.8 free version. Can you please confirm that you can do it in the latest version? Here's the ligand file: https://www.rcsb.org/ligand/LA
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You need to download from https://github.com/oddt/rfscorevs_binary/tree/master. There an option to set the path as shown in https://pyrx.sourceforge.io/pyrx-11-release-announcement/
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Tuncay Karakurt posted a comment on discussion General Discussion
The update is only version 1.0. How do we provide the “rf-score-vs.exe” executable file?
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Hello, Thank you for being PyRx customer. You can use "Help > Check for Updates..." within the PyRx application; this will initiate a search for available updates to your current version. If this doesn't work, you can use the manual procedure described in https://pyrx.sourceforge.io/recent-changes-in-vina-web-services-and-mac-os-x-updates/ The 1.1 version includes a new “rf-score-vs.exe” executable, that you'll need to download separately.
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Hello ; I am using the licensed version 0.9.8. Can I update it to version 1.1 for free?
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Please purchase the latest version. If this bug is there, I'll fix it and give you a refund.
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Abu Hurayra Emad posted a comment on discussion General Discussion
how to solve this problem on pyrx?
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added bndIndex
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Shofia posted a comment on ticket #91
I'm really grateful for your help #Sarkis Dallakian. Now my autodockwizard can be used. I wish you a happy day and success in all your work.
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Try renaming the ligand with a shorter name.
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Autodockwizard can't running
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use EVT_CONTEXT_MENU since the original was not working with py3
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py3 fixes
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adding requiments
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From https://pyrx.sourceforge.io/faq#cluster PyRx enables Cluster execution mode when, in addition to AutoDock binaries, you also have qsub (PBS or SGE) in your path. Please install PyRx on the head node and make sure that AutoDock binaries are available from all the nodes. PyRx creates individual job files for each protein-ligand docking and submit all the jobs to your cluster. Does this answer your question?
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Abhishek Chowdhury posted a comment on discussion General Discussion
I'm using PyRx on a 16-core desktop running on Linux. However, it would take me ages to screen the millions of compounds which I have. I have got access to a 96-core local cluster but I'm struggling to find a detailed tutorial on how to set up PyRx on cluster. Can PyRx jobs be run on a local cluster through the desktop PyRx GUI or it has to been installed on the cluster and run through command line?
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Hi, where did you get /home/koby/Y/bin/vina from? Does it segfault if you run it by itself? You might need to compile Vina from the source.
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