VMD-L Mailing List
From: Jeff Saxon (jmsstarlight_at_gmail.com)
Date: Fri Nov 06 2020 - 09:52:57 CST
- Next message: Jeff Saxon: "Re: Analysis of DLG filles"
- Previous message: Jeff Saxon: "Re: Analysis of DLG filles"
- Maybe in reply to: John Stone: "Re: Analysis of DLG filles"
- Next in thread: Jeff Saxon: "Re: Analysis of DLG filles"
- Reply: Jeff Saxon: "Re: Analysis of DLG filles"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
hello Simone,
thank you very much for your quick feedback!
Today I tested it on windows and actually could not even complete the
tutorial. I am going to test it on my MAC OX now.
One question - is the name of DLG files should be arranged in some
fixed format matching the name of the protein something like
x_x_nameProt.dlg ? Is it possible to recluster many DLG filles
combined together (loaded from the same directory) based on the RMSD
of the selected region of the ligand (e.g. center of its mass)?
Thank you in advance!
J
пт, 6 нояб. 2020 г. в 15:07, Simone Aureli <simone.aureli_at_usi.ch>:
>
> Hi Jeff,
>
> I'm Simone, the main developer of DDT. Are you using DDT on Windows or Mac/Unix?
> Because not all functionalities have been implemented on Windows.
>
> Anyway, I suggest you to put only the .dlg files and the protein.pdb file inside your Working Directory (WD).
>
> For any issue, please write me.
>
> P.S.: here there is a video-tutorial --> https://www.youtube.com/watch?v=5eR46V7_uKM&list=LL&index=109
>
> Best,
> Simone
> ________________________________
> Da: Jeff Saxon <jmsstarlight_at_gmail.com>
> Inviato: venerdì 6 novembre 2020 14:40
> A: Paolo Conflitti <paolo.conflitti_at_gmail.com>
> Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>; Aureli Simone <simone.aureli_at_usi.ch>
> Oggetto: Re: vmd-l: Analysis of DLG filles
>
> Great, thank you so much!
> could you give me contacts of this person please?
> Actually, I've loaded plugin :-0 but it could not load input DLGs with
> following error (i am using tutorial!)
> no files matched glob pattern "*-Trypsin.pdb"
> no files matched glob pattern "*-Trypsin.pdb"
>
> although I am sure that I am doing everything correctly...
>
> пт, 6 нояб. 2020 г. в 14:26, Paolo Conflitti <paolo.conflitti_at_gmail.com>:
> >
> > Hi Jeff,
> >
> > yes, that plugin allows you to work directly with dlg files and it has a
> > reclustering function.
> > Simone, who is actually maintaining the plugin, can fill you in on other
> > functionalities and maybe help you with your issue.
> >
> > Best,
> > Paolo
> >
> > Il 06/11/2020 13:27, Jeff Saxon ha scritto:
> > > thank you Paolo!
> > > It seems that there is a problem with the plugin. I've just tried to
> > > install it with my vmd 1.9.3 (on windows) following all of the
> > > instructions and although it appeared in the Analysis menu, while
> > > clicking on it I got an error message from VMD
> > > vmd > ERROR) Creation of window for 'ddt' failed (invalid command name
> > > "ddt_tk").
> > > mb I should try with my mac version of VMD
> > > anyway does it allow to work directly on DLG filles and do some
> > > operations on it (combining, reclustering)?
> > > Thanks in advance!
> > >
> > > пт, 6 нояб. 2020 г. в 10:00, Paolo Conflitti <paolo.conflitti_at_gmail.com>:
> > >> Hi,
> > >> There is a plugin called Drug Discovery Tool (DDT) that is available
> > >> here: https://sites.google.com/site/vittoriolimongelli/downloads.
> > >>
> > >> Best regards,
> > >> Paolo Conflitti
> > >>
> > >> Il 05/11/2020 17:45, Jeff Saxon ha scritto:
> > >>> Dear VMD users!
> > >>> Could you tell me whether there is some vmd's plugin that allows me to
> > >>> read directly DLG filles (produced by autodock) and make some basic
> > >>> operations on the conformational ensembles of the ligand?
> > >>> I've tried to load directly DLG files from terminal command line
> > >>> vmd *.dlg
> > >>> but it recognized it as an attempt to load PDB files and eventually did nothing.
> > >>>
> > >>> Thank you for your help
> > >>> J.
> > >>>
- Next message: Jeff Saxon: "Re: Analysis of DLG filles"
- Previous message: Jeff Saxon: "Re: Analysis of DLG filles"
- Maybe in reply to: John Stone: "Re: Analysis of DLG filles"
- Next in thread: Jeff Saxon: "Re: Analysis of DLG filles"
- Reply: Jeff Saxon: "Re: Analysis of DLG filles"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]