Re: Calculate energy of a residue using NAMD energy

From: Onur Serçinoğlu (onursercin_at_gmail.com)
Date: Thu Feb 01 2018 - 06:06:08 CST

Hi Monika,

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

I'm not 100% sure, but could it be that namdenergy can't locate the namd2
executable? After all, the plugin utilizes namd2 exe to calculate the
energy of a given residue and you need to provide the path to the
executable if namd2 isn't in the executable search path of your system.

When calling namdenergy, try this:

namdenergy -all -sel $sel -par myparameterfile.inp -exe pathtothenamd2exe

Replace pathtothenamd2exe with the full path of namd2 exe in the remove
server.

Best,
Onur

2018-02-01 2:25 GMT+03:00 Monika Madhavi <monikamadhavi_at_gmail.com>:

> Hi Peter,
>
> I am using VMD installed on the cluster so I have no idea whether they
> have installed the latest version. I used the syntax given in the link you
> sent but, that's the error I get. May be I should first try the script with
> VMD on my personal computer so that I can track the error.
>
> Thanks anyway.
> Best,
> Monika
>
> On Wed, Jan 31, 2018 at 12:51 PM, Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
>> Dear Monika,
>> namdenergy is a proper vmd plugin. Is there any reason that you're trying
>> to use an old downloaded version rather than using the package that comes
>> with vmd?
>> package require namdenergy
>> should make the text interface available. See
>> http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/ for how to use
>> it.
>> Best,
>> Peter
>>
>> 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-7
>>> 277/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.
>

This archive was generated by hypermail 2.1.6 : Thu Dec 05 2019 - 23:19:33 CST