VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Mar 30 2015 - 09:26:26 CDT

It appears that there is something amiss with the parameter file(s) you're passing into NAMDEnergy via the -par option. The error message suggests that one of the dihedral parameters contains a periodicity of zero (n=0). Normal values are 1, 2, 3, 4, and/or 6.

Regards,
Christopher Mayne

On Mar 30, 2015, at 12:26 AM, Subrata Paul wrote:

Dear NAMD/VMD user,

I am calculating nonbonded energy from amber topology file usind VMD NAMDenergy plugin.
The following error are coming

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: The periodicity of dihedral # 1 is zero!

Charm++ fatal error:
FATAL ERROR: The periodicity of dihedral # 1 is zero!

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: The periodicity of dihedral # 1 is zero!

Charm++ fatal error:
FATAL ERROR: The periodicity of dihedral # 1 is zero!

    while executing
"exec $namdcmd ${jobname}-temp.namd > ${jobname}-temp.${i}.log"
    (procedure "namdrun" line 75)
    invoked from within
"namdrun"
    (procedure "namdmain" line 76)
    invoked from within
"namdmain"
    (in namespace inscope "::namdEnergy" script line 19)
    invoked from within
"::namespace inscope ::namdEnergy {
      mol top $currentMol
      variable sel1
      variable sel2
      variable nsel
      set energy ""
      set..."
    invoked from within
".namdenergy.gobutton invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 22)
    invoked from within
"tk::ButtonUp .namdenergy.gobutton"
    (command bound to event)

Can you suggest me why..? 

--
With Best Regards
Subrata Paul
PhD Student
Dept of Chemistry.
IIT Guwahati