tag:blogger.com,1999:blog-7844526396210378482.post1928330202152088044..comments2024-01-31T09:23:26.925+00:00Comments on Noel O'Blog: PyRx - AutoDocking made simpleNoel O'Boylehttp://www.blogger.com/profile/03288289351940689018noreply@blogger.comBlogger11125tag:blogger.com,1999:blog-7844526396210378482.post-23898956191438222752020-06-08T16:54:54.041+01:002020-06-08T16:54:54.041+01:00This post is 9 years old. I don't remember wha...This post is 9 years old. I don't remember what the idea is behind step 3. It must have been to get newer versions of some of the source files, and so this may no longer be necessary. Those links were to the source code repository of PyRx, and are now broken.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-26515666175969218402020-06-08T14:39:58.367+01:002020-06-08T14:39:58.367+01:00Dear Author,
Thank you for this tutorial.
What do ...Dear Author,<br />Thank you for this tutorial.<br />What do you mean by item (3): Replace the appropriate file in "C:\Program Files (x86)\PyRx\Lib\site-packages\PyRx" with importWizard.py, dbPlot.py and autodockNavigator.py.<br /><br />After install the files exists?<br />Thanks,<br />KarimKarimnoreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-43512854227644997412014-02-10T10:40:43.867+00:002014-02-10T10:40:43.867+00:00Dear Sir!
I am using the AutoDock Vina in PyRx 0.7...Dear Sir!<br />I am using the AutoDock Vina in PyRx 0.7.<br />Is it possible to get the protein-ligand complex after docking, so that i can proceed for the molecular dynamic simulation of the same.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-64880803664953831652013-09-03T13:54:06.609+01:002013-09-03T13:54:06.609+01:00hi Sir, i have a problem in i workspace tarball, h...hi Sir, i have a problem in i workspace tarball, how can prepare this file,<br />i have sdf compound library and receptor protein molecule, i want to do virtual screening of ligands molecules.<br /><br />Anonymoushttps://www.blogger.com/profile/18355249057592850694noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-11204211830368277542013-07-19T14:16:26.487+01:002013-07-19T14:16:26.487+01:00I don't know what is the maximum size of the p...I don't know what is the maximum size of the protein molecule that that can be docked using PyRx, since I didn't hit that limit. With 64-bit version of AutoDock, you are practically limited by how much RAM you can afford. <br /><br />Please visit <a href="http://pyrx.sourceforge.net/" rel="nofollow">http://pyrx.sourceforge.net</a> and click on <a href="http://sourceforge.net/donate/index.php?group_id=280633" rel="nofollow">Support This Project</a> on top left, if you need email support.Sargishttps://www.blogger.com/profile/01730048467387998912noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-88908829806159682332013-07-19T10:31:04.733+01:002013-07-19T10:31:04.733+01:00I could not find any e-mail address to contact the...I could not find any e-mail address to contact them..can you provide me the e-mail address to which i should contact?Anonymoushttps://www.blogger.com/profile/05875066600037294859noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-58822318220149273882013-07-19T10:22:42.238+01:002013-07-19T10:22:42.238+01:00You should contact PyRx for help...You should contact PyRx for help...Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-25783607651958056912013-07-17T10:32:30.620+01:002013-07-17T10:32:30.620+01:00I want to ask the maximum size of the protein mole...I want to ask the maximum size of the protein molecule (amino acid residues)that can be docked using PyRx?Anonymoushttps://www.blogger.com/profile/05875066600037294859noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-87302171704038468602012-06-22T12:15:44.970+01:002012-06-22T12:15:44.970+01:00You should contact PyRx for help...You should contact PyRx for help...Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-76380571093381402282012-06-20T17:07:07.565+01:002012-06-20T17:07:07.565+01:00Hi Noel
I did exactly like you mentioned in the ...Hi Noel <br /> I did exactly like you mentioned in the blog for installing Pyrx (0.8) in windows xp.<br />But i am getting error as below:<br /><br /><br />Error running "C:\Program Files x(86)\Pyrx\vina.exe" --config conf.txt --ligand..\..\Ligands\test.pdbqt<br /><br /><br />Stderr" 'C:\Program' is not recognized as an internal or external command,operable program or batch file<br /><br />Any help is greatly appreciated.sahhttps://www.blogger.com/profile/17757064924890723903noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-61086618058706504612011-04-04T21:57:41.175+01:002011-04-04T21:57:41.175+01:00Thank you very much Noel! PyRx owes a great deal t...Thank you very much Noel! PyRx owes a great deal to <a href="http://openbabel.org" rel="nofollow">Open Babel</a> and other open-source programs including AutoDock 4.2 and Vina. <br /><br />Many Medicinal Chemists are overwhelmed with a rather high barrier of entry into docking and virtual screening. A recent article on <a href="http://pubs.acs.org/doi/abs/10.1021/jm100164z" rel="nofollow">Cheminformatic Tools for Medicinal Chemists</a> puts virtual screening under Unknown Unknowns <br />and in the domain of the expert computational chemist. <br /><br />I hope that tools like PyRx would lower barriers of entry for medicinal chemists and make virtual screening useful cheminformatic tool in practice.<br /><br />Cheers!Sargishttps://www.blogger.com/profile/01730048467387998912noreply@blogger.com