VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 22 2019 - 17:30:33 CST

Looking at the git repo, that appears to be the David Rogers' research group's
githube repo, and they have made what appears to be a own fork of the pbctools
code. That being said, if you want to use this particular fork
of the code, you're going to want to contact them for tech support, since I
haven't heard anything about it prior to today. ;-)

Just because there's a github page doesn't guarantee that you've
found an official version of software that anyone is going to support.
If people fork the open source VMD plugins and don't tell us about it,
we can't really do much to help users with these special versions.

It looks like they revised the code with new changes beyond what's
in the current version included with VMD, but as I say, nobody has
contacted me about it prior to today, so I'm currently unfamiliar
with their work. I will look at it more closely next week.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Feb 22, 2019 at 10:28:37PM +0000, Tripathi, Ashutosh wrote:
> Shall I just then download
>
> The package [1]PBCtools (v1.1 or later) from the VMD script library..?
>
> Earlier I downloaded the pbctools from
>
> [2]https://github.com/frobnitzem/pbctools
>
> Many thanks!
>
> Ashutosh
>
> --------------------------------------------------------------------------
>
> From: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> Sent: Friday, February 22, 2019 4:15:14 PM
> To: vmd-l_at_ks.uiuc.edu; Tripathi, Ashutosh
> Subject: RE: [EXTERNAL] RE: pbctools installation error
>
> Hi Ashutosh,
>
> Yeah, that happens because .so is the default file extension for compiled
> shared object libraries on unix-derived operating systems (Linux & Mac).
> Those files have zero meaning on windows systems, which instead uses .dll
> files for the same purpose. The immeadiate solution to your problem is to
> go back to the version of pbctools distributed with VMD that only depends
> on tcl and forget this ever happened. Was there a particular feature you
> were looking for that wasn't in the standard build?
>
> -Josh
>
>
>
> On 2019-02-22 15:10:36-07:00 Tripathi, Ashutosh wrote:
>
> It mentioned:>
>
>
>
> "C:/Softwares/VMD/pbctools couldn't load library
> "C:/Softwares/VMD/pbctools/libpbc_core.so": this library or a dependent
> library could not be found in library path 3.0"
>
>
>
> I tried looking up for libpbc_core.so file but couldn't find it
> anywhere.
>
>
>
> Thank you so much
>
>
>
> Ashutosh
>
>
>
>
>
> From: "Vermaas, Joshua" <Joshua.Vermaas_at_nrel.gov>
> Date: Friday, February 22, 2019 at 4:05 PM
> To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>, "Tripathi, Ashutosh"
> <tripathi_at_medicine.tamhsc.edu>
> Subject: [EXTERNAL] RE: pbctools installation error
>
>
>
> A .so file on windows shouldn't be required. What did it specifically
> say?
>
> -Josh
>
>
>
>
> On 2019-02-22 14:36:43-07:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>
> I recently installed VMD version 1.9.3 on my Window's workstation (Windows 7). I am now trying to install PBCtools plugin which I downloaded from github. I have made modifications to the vmd.rc file.
>
>
>
>
>
> set dir C:/Softwares/VMD/pbctools
>
> source $dir/pkgIndex.tcl
>
> package require pbctools
>
>
>
>
>
> However, VMD cannot load libpbc_core.so library files. it specifically says
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbctools/
> 2. https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_frobnitzem_pbctools&d=DwMF-g&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=JBqQLS7jZ5whrB0hXJY8MNYcfDrh8UhlGJ2ANxoi8s0&m=KmBm3Wx8GvoHF--cErOpnDw-gziq8qmVXSMJSTFnbyY&s=LuHlgs3doHGcAUE65ehpkI_vLtWDd1QSiyzwqX7uc70&e= 

-- 
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/