reading output files (pdbqt) from an external vina dock run back into chimera
Hello is there a way of reading a series of pdbqt files of docked ligands using vina dock externally back into chimera for inspection and analysis? It looks like Viewdock, should do this but I have a directory full of individual ligand files and I don't know how to prepare them so that Listview reads them into an ordered set i.e. ligand1 ligand2 etc. I can read individual ligands fine. Many thanks Joern
Hi Joern, I'm not sure to understand, but you can simply open the files, since they are in pdb format. Best, Marco Il 19/03/2022 13:05, Joern Werner via Chimera-users ha scritto:
Hello
is there a way of reading a series of pdbqt files of docked ligands using vina dock externally back into chimera for inspection and analysis? It looks like Viewdock, should do this but I have a directory full of individual ligand files and I don't know how to prepare them so that Listview reads them into an ordered set i.e. ligand1 ligand2 etc. I can read individual ligands fine.
Many thanks Joern
_______________________________________________ Chimera-users mailing list:Chimera-users@cgl.ucsf.edu Manage subscription:https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
-- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail:sette@uniroma2.it e-mail:m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette Ai sensi del Regolamento (UE) 2016/679 e dei principi contenuti nelle linee guida del Garante per posta elettronica e interne (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell’amministrazione digitale) si precisa che le informazioni contenute in questo messaggio -come pure i dati esteriori delle comunicazioni e i file allegati- sono riservate e ad uso esclusivo del destinatario. Divulgazione, copia, stampa o qualunque altro uso da parte di altri non è autorizzato. Qualora il messaggio in parola Le fosse pervenuto per errore, La preghiamo di eliminarlo senza copiarlo e di non inoltrarlo a terzi, dandocene gentilmente comunicazione al seguente indirizzo e-mailprivacy@uniroma2.it. On the basis of “(UE) Rules 2016/679 and the codes in general guidelines of Garante for electronic and internal mail (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell’amministrazione digitale) information here contained and any attachments is confidential and intended for the recipient(s) only. Dissemination, copying, printing or use by anybody else is unauthorized. If you are not the intended recipient, please delete this message and any attachments and advise the sender by return e-mail toprivacy@uniroma2.it.
Hello Joern, As far as I can recall, Autodock Vina will (or at least has a choice to) put all the ligand docking results, i.e. multiple poses and/or compounds, in a single pdbqt file. I don't have the program currently, so I can't say anything specifically about how to control it. If all you have now is a lot of separate models, you could try opening them all, and then saving them to a single multi-model PDB file and reopening that single PDB file with ViewDock. However, that would lose all of the extra information in the pdbqt file, certainly the charge/radius columns, and also perhaps all of the scores and other other descriptors output by docking. Thus it would be better if you could get the single-file output directly from the docking program. saving PDB files from Chimera <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 19, 2022, at 5:05 AM, Joern Werner via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello
is there a way of reading a series of pdbqt files of docked ligands using vina dock externally back into chimera for inspection and analysis? It looks like Viewdock, should do this but I have a directory full of individual ligand files and I don't know how to prepare them so that Listview reads them into an ordered set i.e. ligand1 ligand2 etc. I can read individual ligands fine.
Many thanks Joern _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Joern Werner -
Marco Sette