From: Ashar Malik (
Date: Fri Dec 05 2014 - 00:03:26 CST

Hi Sujata,

>From the charmm topology;

Hydrogen on Beta carbon has charge of 0.09
Oxygen on Asp - side chain is -0.76.

I haven't used measure energy but i think that if you don't provide the
charge information (q1 & q2) - they would be obtained from the PSF file
(atom type). Which in the above case - would make sense if they are
repulsive (not sure why though) however when you specify q1 and q2 you are
giving them charges - which are opposite (and unrealistic - could you
explain why you chose those charges) so naturally there would be a
favourable interaction between them. I haven't used measure for the
calculations of energies - but I would still recommend using "namdenergy".

you can use it in a tcl script to implement it:
here is an excerpt from my script:

package require namdenergy
namdenergy -nonb -sel [atomselect top "segname P1 and resid 3"] [atomselect
top "nucleic"] -norun -extsys ../../equil_npt.xsc -pme -par

In the above two selections are passed - to namdenergy, 1 complete residue
and a stretch of DNA that is close to it - for calculation of the -non
bonded energies only in a MD trajectory I already have. You can do the same
on 1 frame as well (I think - never tried it but it should work).

There is a discussion earlier in the mailing list - here:

which may also be helpful.