PyRx output structures

[seema]

It was love at first sight with PyRx. For the first time since struggling with Autodock, ADT and others, I could get a beautifully docked first structure. Congratulations, Sargis. But please tell me how to get the receptor structure along with the docked ligand in the output file.Please. And pray, never think of making this software commercial.

[sargis]

Thank you for the message. I'm glad you liked PyRx and I'm excited to hear about PyRx success stories. Saving the receptor structure along with the docked ligand is not implemented yet. This is because it's a low priority since one can copy/paste the receptor structure text into the output file to get the desired result.

Regarding making this software commercial: I'm currently not getting any financial support for developing PyRx. I've opted-in to receive donations at http://pyrx.sourceforge.net, but I haven't got any and don't expect donations any time soon. I'm thinking to charge for new Windows and Mac installers in a couple of years if need be. I'm also open to new projects and collaborations.

Thank you for using PyRx!

[seema]

Hi Sargis,

Thank you for your tips to get the receptor structure. Cannot you get a big grant from NIH or any good funding agency, telling them about its success stories? Making it commercial for academics will be huge disadvantage, as it will hinder the progress of scientific work. AutoDock's popularity is just because it is free and reliable too at the same time. Wish you get a big grant to help maintain the software.

[seema]

Hi Sargis,

Can you please tell me where to put the copy-pasted receptor coordinates in the .sdf file of the ligand? I tried to put at the end or the beginning of the docked ligand coordinates but could not figure out. Trivial question this one.

[sargis]

Can you please tell me where to put the copy-pasted receptor coordinates in the .sdf file of the ligand? I tried to put at the end or the beginning of the docked ligand coordinates but could not figure out. Trivial question this one.

Hi Seema,

To paste receptor coordinates in the .sdf file of the ligand, you'll need to make .sdf for the receptor first. You can use Open Babel to convert pdb to sdf. You can do all this with PyRx or use a combination of other tools. You can also use -j option in babel to join input molecules into a single output molecule - http://openbabel.org/wiki/Tutorial:Basic_Usage

Best wishes.