From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Nov 02 2015 - 10:51:24 CST

On Mon, Nov 2, 2015 at 4:06 AM, sunyeping <sunyeping_at_aliyun.com> wrote:
>
> Dear all,
>
> I am trying to use VMD plugin namdenergy to calculate the interaction
> potential between each reside of one segname of a protein with anoher
> segment of the protein, and write the results into a series of files. The
> following is the script:
>
> set sel1 [atomselect top "segname P3"]
> set sel2 [atomselect top "segname P1"]
> set n [llength [lsort -unique [$sel1 get resid]]] ;#return the number of the
> residues in segment P3
> set n0 [lindex [lsort -unique [$sel1 get resid]] 0] ;#return the index of
> the first residue of segment P3
> for {set i $n0} {$i<=$n} {incr i} {
> set file [open output$i.dat w] #generate an empty file for writing the
> calculation results of interaction energy between segment P1 and residue $i
> of segment P3
> set sel3 [atomselect top "segname P3 and resid $i"]

looks to me as if you need to read the namdenergy plugin documentation
more carefully. especially the following line:

Output file (-ofile FILE): Gives the name of the file for final energy
output to be printed to. If not specified, output will be printed to
the vmd console.

> namdenergy -ofile $file -vdw -elec -nonb -sel $sel3 $sel2 -tempname namd -switch 10 -cutoff 12

this line offers the name of the *file object* (so typically something
like file2 or file3) as argument.
if you want it to write to the file named output<frameno>.dat the line
would have to be:

 namdenergy -ofile "output$i.dat" -vdw -elec -nonb -sel $sel3 $sel2
-tempname namd -switch 10 -cutoff 12

and you *must* not open and close that file yourself, as that would
create an access conflict and leave it to chance whether you get to
see the output or an empty file.

axel.

> close $file
> }
>
> However, when I source the script in VMD console, the files are indeed
> generated, and the namdenergy calculation are perfomed, but all the output
> files are empty until the calculation is finished. So what's wrong with the
> scripts?
>
> Thank you in advance.
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.