Re: Calculate energy of a residue using NAMD energy

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Tue Jan 30 2018 - 17:41:28 CST

Dear all,

Thank you for the responses. I tried the script again with "package require
namdenergy" and solved half of the problem I guess. However, the output now
looks like,

 namdEnergy) Running
namdEnergy) namd-temp.namd

*couldn't execute "": no such file or directory*

I thought the error is coming from the parameter file I specified but the
log says the parameter file is taken into consideration. The error is there
even if I use the default parameter file. Looks like a minor thing but it
is still not working. Any insight is appreciated.

Thanks.
Monika

On Wed, Jan 31, 2018 at 1:18 AM, Brian Radak <brian.radak_at_gmail.com> wrote:

> Are you running this with VMD?
>
> The Tcl environments for VMD and NAMD are different - if using NAMD my
> guess is that none of those "package require" commands are working
> correctly.
>
> It requires some modest scripting, but I believe you can do what you want
> in NAMD using the pairInteraction keyword (user guide p. 222) along with
> the coorFile (which probably deserves more bold documentation, user guide
> p. 18).
>
> On Mon, Jan 29, 2018 at 10:22 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
> wrote:
>
>> Dear all,
>>
>> I want to calculate the total energy of a specific residue (a water
>> molecule) at each frame. It is suggested that this can be done using NAMD
>> energy plugin. However, I would like to do the job through a script because
>> my trajectory is in a remote server.
>>
>> I tried the following.
>> obtained the code in this link and created a .tcl file called
>> namdenergy.tcl in the folder where I have my script.
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-
>> 7277/namdenergy.tcl
>>
>> Then I wrote a different tcl script with
>> source namdenergy.tcl
>> namd energy -all -sel $sel -par myparameterfile.inp
>>
>> Here I specified the parameter file because my parameter file is
>> different from the common charmm parameter file. However, I am getting the
>> following error
>>
>> invalid command name "::FinderTool::find"
>>
>> I would be grateful for a guidence to correctly use the namd energy to
>> calculate energies of some selected atomselections.
>>
>> Thank you.
>> Best,
>> Monika
>>
>> --
>> W.A.Monika Madhavi
>> Lecturer (Probation),
>> Department of Physics,
>> University of Colombo.
>>
>
>

-- 
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.

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