From: gagandeep singh (gagan.sk.1994_at_gmail.com)
Date: Wed May 27 2020 - 18:33:12 CDT

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 pluginsset 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
>
>
>
>
>
>