VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Mar 28 2013 - 17:19:01 CDT

Hmm... What it is yelling at you for is an unreadable psf file, which
seems odd. Is it possible that you didn't load the psf into the molecule
you tried to run NAMD energy on? PDB and dcd files have no information
as to what the bond, angle and dihedral lists are, which is information
contained in the psf and is needed for running namd. If you did load the
psf into your molecule, what are the contents of the /.namd/file
NAMDenergy generated and tried to run (usually called
namdenergy-temp.namd or something like that in VMD's working directory)?
-Josh

On 03/28/2013 05:06 PM, Anurag Sharma wrote:
> Hi Josh,
>
> Thanks for the reply. I have done the same. But as I mentioned in
> later part of my ques. When I specify the path it gives me other
> error. I uninstalled and re-installed the software but still not
> figure what is the exact problem.
>
> Anurag
>
> Sent from my iPhone
>
> On Mar 28, 2013, at 4:57 PM, "Josh Vermaas" <vermaas2_at_illinois.edu
> <mailto:vermaas2_at_illinois.edu>> wrote:
>
>> Hi Anurag,
>>
>> You need to specify where a namd2 binary is, usually the same
>> executable that you used to run the simulation. For instance, on my
>> machine at home, I have my NAMD folder on the desktop, and so the
>> path in my case would be C:\stuff-I-don't-remember\Desktop\NAMD,
>> which is the folder with the namd2 binary in it.
>>
>> -Josh
>>
>> On 03/28/2013 03:25 PM, Anurag Sharma wrote:
>>>> /Dear VMD users, /
>>>>
>>>> / /
>>>> /I work with VMD 1.9.1 on a Window7 platform and have used it for
>>>> MD simulations//. Upon using the NAMD Energy to measure
>>>> the //interaction.//I clicked the "Run NAMDEnergy" and got
>>>> a //message that: /
>>>> /"Program not found /
>>>> /Could not locate 'namd2' /
>>>> /Description: NAMD 2.x Molecular Dynamics Engine /
>>>> /Would you like to specify its path?" /
>>>> / /
>>>> /If I do not specify the namd file I get "Error: couldn't execute
>>>> "": no /
>>>> /such file or directory" /
>>>> / /
>>>> /When I do specify the namd2.exe file in \NAMD_2.9\, I get an error /
>>>> /"Error: Processor 0 exiting: Called Cmi Abort /
>>>> /Reason: FATAL ERROR: UNABLE TO OPEN .psf FILE
>>>> I:��ResearchSnapshots and datasnapshots and
>>>> dataSnapshotsfilename?pcl rial_8Energyfilename.psf/
>>>>
>>>> / while executing
>>>> "exec $namdcmd ${jobname}-temp.namd > ${jobname}-temp.log"
>>>> (procedure "namdrun" line 56)
>>>> invoked from within
>>>> "namdrun"
>>>> (procedure "namdmain" line 76)
>>>> invoked from within
>>>> "namdmain"
>>>> (in namespace inscope "::namdEnergy" script line 19)
>>>> invoked from within
>>>> "::namespace inscope ::namdEnergy {
>>>> mol top $currentMol
>>>> variable sel1
>>>> variable sel2
>>>> variable nsel
>>>> set energy ""
>>>> set..."
>>>> invoked from within
>>>> ".namdenergy.gobutton invoke"
>>>> ("uplevel" body line 1)
>>>> invoked from within
>>>> "uplevel #0 [list $w invoke]"
>>>> (procedure "tk::ButtonUp" line 24)
>>>> invoked from within
>>>> "tk::ButtonUp .namdenergy.gobutton"
>>>> (command bound to event)//" /
>>>> / /
>>>> /What should I do? /
>>>> /Thanks for the help /
>>>> / /
>>>> /Anurag /
>>>>
>>