It is most likely the spacing setting in PMV (it is set to the default value used by the original Autodock, namely 0.375A). In Autodock Vina it should be set to 1 angstrom.
Let me know if this helps Kind regards, Sorin On Sun, Nov 19, 2023 at 1:57 PM BRUNO DI GERONIMO QUINTERO < brunodigeron...@ucm.es> wrote: > Hello Thripthi S. , > > Given the information you provide, it is quite difficult to figure out > what your issue is with VINA. If you provide me the data (receptor, ligand, > and box), I can do some tests, to see what's happening. In VINA, *pdbqt > files for both receptor/ligand are the most tricky part to parameterize > before performing the docking *per se.* > > On the other hand, Maestro is more friendly software and straightforward > than VINA. > > Best regards, Bruno > > El dom, 19 nov 2023 a las 13:35, Thripthi Shenoy (< > thripthishe...@gmail.com>) escribió: > >> Greetings to all, >> >> I have performed docking through Glide and Autodock vina for a protein >> for which the active site has been taken from the literature. Glide is able >> to dock the compounds correctly in the active site whereas autodock vina >> does not dock the compounds within the specified site. I have tried docking >> several times in Autodock vina, but not able to obtain proper results. >> I would be grateful to receive any suggestions regarding the same. >> >> Thanking you in advance, >> Thripthi S. >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
