VMD-L Mailing List

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Wed Dec 02 2015 - 17:41:25 CST

The issue is that the element fields get filled with seemingly random X characters when the pdbqt file is read in. Attached is a 10mer of a pdbqt protein file. Ligand pdbqt files are riddled with other non-standard keywords. Brian ________________________________________ From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of John Stone [johns_at_ks.uiuc.edu] Sent: Wednesday, December 02, 2015 2:51 PM To: Gustavo Seabra Cc: vmd-l_at_ks.uiuc.edu Subject: Re: vmd-l: Problem visualizing a pdbqt file generated by AutoDockTools Hi, If someone can send me a few of these .pdbqt files as examples, I can probably add a molfile plugin that will read them so that VMD 1.9.3 would read these directly without needing to edit anything in the files. If you guys can gzip/zip up a few examples, I'm happy to give it a shot. Cheers, John Stone vmd_at_ks.uiuc.edu On Wed, Nov 25, 2015 at 03:27:52PM -0300, Gustavo Seabra wrote: > Brian, > > You are right, removing the last 3 columns did the trick. > > I removed the extra information by using the command: > > :%s/ 1\.00\zs .*// > > inside vim, to remove the extra lines in the protein, then repeating the command substituting the 1\.00 by 0\.00 to remove the lines from the ligand. But after that, all works fine. > > Thanks a lot! > Gustavo Seabra > Gustavo Seabra > > > > > Em 25 de nov de 2015, à(s) 13:51, Bennion, Brian <Bennion1_at_llnl.gov> escreveu: > > > > It can open them as you have seen but without connection records it uses the element field to determine bonding and thereby structure. I think that if you remove the last three columns then you can get connectivity back. > > I will look to see what I did. > > Brian > > > > ________________________________________ > > From: Gustavo Seabra [gustavo.seabra_at_gmail.com] > > Sent: Wednesday, November 25, 2015 8:41 AM > > To: Bennion, Brian > > Cc: vmd-l_at_ks.uiuc.edu > > Subject: Re: vmd-l: Problem visualizing a pdbqt file generated by AutoDockTools > > > > Hi Brian, > > > > Thanks a lot! Apparently, VMD isn?t able to open PDBQT files then. I wonder if there are plans to add this functionality to VMD any time in the foreseeable future. > > > > All the best! > > Gustavo Seabra > > > > > > > >> Em 25 de nov de 2015, à(s) 11:54, Bennion, Brian <Bennion1_at_llnl.gov> escreveu: > >> > >> Hello, > >> I have seen this issue with in my own work a long time ago. Unfortunately I dont remember the exact cause. The format of the pdbqt file in the last 3? columns may confuse/prevent determination of backbone status. The values in those columns are not standard pdb convention. > >> Brian > >> > >> > >> ________________________________________ > >> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Gustavo Seabra [gustavo.seabra_at_gmail.com] > >> Sent: Wednesday, November 25, 2015 4:59 AM > >> To: vmd-l_at_ks.uiuc.edu > >> Subject: vmd-l: Problem visualizing a pdbqt file generated by AutoDockTools > >> > >> Dear all, > >> > >> I?m having a weird problem trying to open a PDBQT file generated by ADT in VMD. VMD can open the file using PDB format, but only displays it as atom-based representations. Whenever I try to visualize using a backbone-based representation (ribbons, cartoon, etc.), nothing shows. Has anyone here dealt with a similar problem before? > >> > >> If anyone wants to try, the file is here: > >> https://www.dropbox.com/s/ybno7ezf60jgboq/Compound14-3U1I.pdbqt?dl=0 > >> > >> Thanks a lot! > >> Gustavo Seabra > >> > >> > >> > >> > >> > > > -- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/