Re: Calculate energy of a residue using NAMD energy

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Thu Feb 01 2018 - 18:08:15 CST

Hi Onur,

Thank you very much for your suggestion. Actually it worked. In the cluster
I loaded both NAMD and VMD modules (earlier I had only VMD loaded) and the
script worked.

However, now I have a different problem. As I mentioned earlier, my task is
to calculate the total energy of a water molecule at a particular frame. So
this is the tcl code I used in vmd to do this.

package require namdenergy
set mol [mol new mypsf.psf type psf waitfor all]
mol addfile mydcd.dcd type dcd first 0 last -1 waitfor all molid $mol
set nf [molinfo $mol get numframes]
for {set frm 0} {$frm < $nf} {incr frm} {
set sel [atomselect $mol "index $indo $indh1 $indh2" frame $frm]
set totalE [namdenergy -all -sel $sel -par "myparameterfile.inp"]
puts $output $totalE

In the output file, value of all the calculated energies are zero. This is
the same if -bond or -elec is used as the energy type.

Thank you.
Best,
Monika

On Thu, Feb 1, 2018 at 10:06 PM, Onur Serçinoğlu <onursercin_at_gmail.com>
wrote:

> 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.
>>
>
>

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

This archive was generated by hypermail 2.1.6 : Tue Sep 17 2019 - 23:19:37 CDT