VMD-L Mailing List

From: lanhua (lh2122_at_columbia.edu)
Date: Fri May 04 2007 - 12:14:55 CDT

Hi,
    I had one problem when I tried to calculate the non-bond interaction between two atom selections by using the following command in the text interface:
>set sel1 [atomselect top "protein and name HN"]
>set sel2 [atomselect top "water and name OH2"]
>$sel1 frame 0
>$sel2 frame 0
>namdenergy -nonb -sel $sel1 $sel2 -switch 10 -cutoff 12 -skip 5 -extsys namd-temp.xsc -pme
      (Where namd-temp.xsc was generated by clicking "Generate" on the NAMDEnergy GUI)
     I was told that "couldn't execute "": no such file or directory". Could you please tell me how to figure it out?
     
         In addition, I am confused about what Peter said here (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/8483.html) about "or write your own script to take the coordinates in vmd and run them through an arbitrary energy function over the trajectory. "
                                                                      
     Thanks a lot!
 
 Best regards,
 Lan