Re: Calculate energy of a residue using NAMD energy

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Thu Feb 01 2018 - 22:51:37 CST

Hi Peter,

Thanks a lot. Yes I was an idiot. I did run with rigid water. What I want
to calculate is the potential energy of a water molecule at a particular
distance from a protein (more specifically, at a hydrogen bonding site).

Best,
Monika

On Fri, Feb 2, 2018 at 1:59 PM, Peter Freddolino <petefred_at_umich.edu> wrote:

> Hi Monika,
> If you ran with rigid water, and you're just calculating the energy of a
> single water molecule alone, it ought to be zero. All of the nonbonded
> interactions are exclusions, and all of the internal interactions are zero
> by definition.
> Are you looking for its interaction with the surrounding system? What is
> the energy that you're trying to calculate?
> Thanks,
> Peter
>
>
> On Thu, Feb 1, 2018 at 7:08 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
> wrote:
>
>> 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.
>>
>
>

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

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