VMD-L Mailing List

From: gagandeep singh (gagan.sk.1994_at_gmail.com)
Date: Wed May 27 2020 - 15:00:35 CDT

Thanks. I will check it out.

On Thu, 28 May, 2020, 1:15 AM Isralewitz, Barry, <isralewi_at_illinois.edu>
wrote:

> Hi Gangdeep,
>
> Since you're after some specific values-- versus exploring analysis
> results -- how about using the "measure sasa" Tcl command directly,
> looping over whatever selections you need for your calculation?
> https://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html
> Cheers,
> Barry
>
>
> On May 27, 2020, at 6:33 PM, gagandeep singh <gagan.sk.1994_at_gmail.com>
> wrote:
>
> Hi Barry Isralewitz
> I tried Timeline plugin but it gives SASA value of each residue. Actually
> I need to calculate the Gibbs free energy of ligand binding binding to the
> protein. The enthalpic and polar contribution is done by MMPBSA and I need
> the *SASA value of each atom* to calculate the Entropic contribution.
>
> @ Giacomo Fiorin
> I added the following in vmd.rc
>
> *########################################################*
> *# set DIR to the location of your WORKING DIRECTORY*
> *########################################################*
> *set dir C:\Program Files (x86)\University of
> Illinois\VMD\plugins\noarch\tcl\vmdICE1.0*
> *source $dir/pkgIndex.tcl*
> *vmd_install_extension vmdICE xrmsdgui_tk_cb "Analysis/vmdICE"*
>
>
>
> Added the following to C:\Program Files (x86)\University of
> Illinois\VMD\scripts\tcl8.5\init.tcl file
>
>
>
> *# Autoload custom plugins set auto_path [linsert $auto_path 0 C:\Program
> Files (x86)\University of Illinois\VMD\plugins] *
>
> Still i am not able to see the vmdICE plugin in the VMD. Am i doing
> anything wrong?
>
> Thanks.
>
> Best,
>
> Gagandeep Singh
>
>
> On Wed, May 27, 2020 at 8:54 AM Isralewitz, Barry <isralewi_at_illinois.edu>
> wrote:
>
>> Hi Gangdeep,
>>
>> You might also try the Timeline plugin, which has a SASA calculation
>> function ("Calculate":"Calc SASA..."). The Timeline plugin is in need of
>> an update to be compatible with the latest Mac Catalina build (and with
>> future builds on other architectures). This update is in progress...
>>
>> Cheers,
>> Barry
>>
>> On May 27, 2020, at 9:39 AM, gagandeep singh <gagan.sk.1994_at_gmail.com>
>> wrote:
>>
>> Dear Giacomo Fiorin
>> I first tried to contact the corresponding author but his email address
>> has been changed and the mail was not delivered to him.
>> I will try to use the way you have recommended and will get back to you.
>>
>> Thanks and regards
>> Gagandeep Singh
>>
>> On Wed, May 27, 2020 at 7:59 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>> wrote:
>>
>>> You could try contacting the developers: seeing as the corresponding
>>> author has since moved to the private sector, that's not guaranteed to
>>> work. Still, have you tried it?
>>>
>>> In general, assuming that a plugin is properly set up with a
>>> pkgIndex.tcl file, one way to let VMD auto-detect it is the auto_path
>>> variable from the Tcl interpreter:
>>> https://wiki.tcl-lang.org/page/auto_path
>>>
>>> # Autoload custom plugins
>>> set auto_path [linsert $auto_path 0 *your_plugins_folder*]
>>>
>>> where *your_plugins_folder *contains one or more plugins, each one in
>>> their subfolder.
>>>
>>> Giacomo
>>>
>>> On Wed, May 27, 2020 at 10:12 AM gagandeep singh <
>>> gagan.sk.1994_at_gmail.com> wrote:
>>>
>>>> Dear All
>>>> I am trying to install vmdICE plugin to calculate the SASA of all the
>>>> atoms in my protein-ligand system, following the steps in the manual but
>>>> unable to successfully install the plugin. I tried in both Windows10 and
>>>> Ubuntu20 to install this plugin in VMD but remained unsuccessful. The
>>>> plugin is not coming up in the analysis section.
>>>> Any help in this regards would be appreciated.
>>>> Thanks and regards
>>>>
>>>> Gagandeep Singh
>>>>
>>>
>>>
>>> --
>>> Giacomo Fiorin
>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>> Research collaborator, National Institutes of Health, Bethesda, MD
>>> http://goo.gl/Q3TBQU
>>> https://github.com/giacomofiorin
>>>
>>
>> --
>> Barry Isralewitz
>> Theoretical and Computational Biophysics Group
>> 3043 Beckman, University of Illinois at Urbana-Champaign
>> Office Phone: (217) 244-1612
>> Email: isralewi_at_illinois.edu <isralewi_at_illinois.edu>
>> http://www.ks.uiuc.edu/~barryi
>>
>>
>>
>>
>>
>>
> --
> Barry Isralewitz
> Theoretical and Computational Biophysics Group
> 3043 Beckman, University of Illinois at Urbana-Champaign
> Office Phone: (217) 244-1612
> Email: isralewi_at_illinois.edu <isralewi_at_illinois.edu>
> http://www.ks.uiuc.edu/~barryi
>
>
>
>
>
>