From: Ravithree Senanayake (rsenana1_at_jhu.edu)
Date: Tue May 14 2024 - 12:48:23 CDT

Hello,

I am trying to use the namdenergy plugin to get the interaction energies between a protein and a mixed membrane. I used the following tcl script to get the interaction energies.

package require namdenergy

package require hbonds

# library is used for obtaining the principal axes

lappend auto_path /home/myusername/la1.0

lappend auto_path /home/myusername/orient

package require Orient

namespace import Orient::orient

set radtodeg 57.2957795131

# load the combined dry production simulation

mol new dry8.psf

mol addfile dry8.dcd waitfor all

# relevant selections

set lip [atomselect top "resname DOPC or resname SAPI"]

#set ligand [atomselect top "resname EG6"]

set prot [atomselect top "protein or resname HEME"]

set nf [molinfo top get numframes]

# energetics (using namdenergy plugin)

namdenergy -sel $lip $prot -ofile lip-prot-energy_test2.txt -switch 8.0 -cutoff 12.0 -par forcefield/par_all36_prot.prm -par forcefield/toppar_all36_prot_heme.str -par forcefield/par_np_water_ions.prm -par forcefield/par_all36_lipid.prm -par forcefield/par_interface.prm -par forcefield/par_all36_carb.prm -par forcefield/toppar_all36_carb_glycolipid.str -elec -nonb -vdw -extsys restart7/restart7.xst -pme -exe ./namd.bash

exit

 From the above script I get nonbonded energy values (electrostatic and vdw) around -500 - -900 kcal/mol which is a very large number when looking into other similar systems.

I noticed that it is the electrostatic energies that are too large and vdw are reasonable.

  1.
May I know if the units of energy are always kcal/mol in namdenergy plugin or if there any conversion I need to take into account?
  2.
Do you see any issues with my namdenergy script here?
  3.
Do you have any suggestions on how to check for any error/mistake with my system/script to debug this issue? (my system looks normal in production runs interms of the dynamics)

Any help would be greatly appreciated,
Best,
R. Senanayake