Solving Major Error in PyRx | Error in converting Macromolecule to pdbqt | Practical Tutorial 

Glad to hear that...

Already have recorded it... ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-mJYIrVNYc-I.htmlsi=LE0k8-iwgcSgpf-T

Thanks for the appreciation...I think you might have missed a step in preparation of your query protein before docking. In chimera or discovery studio there is an option of "add polar hydrogens" to your query protein. Perform that step, I am sure this might resolve your issue...Thanks

Thank you for the quick response. When I am trying to add Hydrogens in chimerax, error: more than 2 coplanar positions specified is displayed. Can you please suggest what to do.

Glad it was helpful!

Glad to hear that!

well...reinstall your pyrx tool because you there is no such issue with your system requirement...thanks

Use autodock VINA option instead of autodock Wizard...This software mostly show error in autodock wizard...No big deal...Results will be same...thanks

You can also fix multiple conformations...method is same...Thanks 4 watching the tutorial...

@@scienceforeveryone8827 i mean if u have a lot of alternate conformations in the pdb file....manual editing will take a lot of time... for example lets consider a pdb id like 5usq

Well I suggest you to go for the manual editing. Secondly, you can also reconstruct the PDB file via using iTESSOR tool. First find the actual amino acid sequence and predict the structure via the above mentioned tool. Doing this will make your research work more precise and impressive. Thanks

Well, I suggest to carefully observe the changes you made...Thanks

Using PyRx tool for docking requires your protein should be completely normalized (prepared). You can use discovery studio or Chimera to prepare your protein. In discovery studio, remove all the ligands, Hetatoms and subunits of your protein that does not have the active sites. Save it as PDB file and load it to PyRx. In chimera remove all the ligands and normalize it on 100 points. It will take time bur will completely normalized. Thanks

Same issue

sorry...i couldnt get your query...

@@scienceforeveryone8827 You mentioned is that after add Macromolecules, then go to CDK1 file, this is query. I dont have CDK1. How to slove it, pls let me know. I have a assignment to submit it

Sorry for the late rply, i was not notified...first you have to download CDK1 protein from Uniprot or Protein data Bank in pdb. format, then you can begin your procedure. Thanks

No issue maim... if you are familiar with the problem, than just follow the steps...It will resolve your issue... Thanks

@@scienceforeveryone8827 That works Alhamdulillah ! Thank you so much sir JazakaAllah khayr

I m glad that it helped u... Its software error...Amino acids are mislebbled.

@@scienceforeveryone8827 thank you for replying My doubt has solved