VMD-L Mailing List

From: Jeff Saxon (jmsstarlight_at_gmail.com)
Date: Fri Nov 06 2020 - 10:53:32 CST

p.s. just double checked with VMD1,9.3 on my MAC and there is the same error
with tutorial files I got

no files matched glob pattern "*-Trypsin.pdb"
no files matched glob pattern "*-Trypsin.pdb"

I can't understand why it was looking for PDB files but not dlg ?? I
guess here it use glob to load all DLG filles from the directory (in
my case it was filled only with DLGs) I also tried to use it with the
directory containing only one DLG but again the same strange error.
J.

пт, 6 нояб. 2020 г. в 16:52, Jeff Saxon <jmsstarlight_at_gmail.com>:

>
> 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.
> > > >>>