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