VMD-L Mailing List

From: Subrata Paul (paul.subrata34_at_gmail.com)
Date: Mon Mar 30 2015 - 13:39:02 CDT

Dear Christopher

Actually, I have load amber parameter and trajectory file in VMD and
try to calculate the vdw energy from the NAMDenergy plugin.

Can you explain me, what is offending entry in parameter file ?

On Tue, Mar 31, 2015 at 12:00 AM, Mayne, Christopher G <cmayne2_at_illinois.edu
> wrote:

> Please CC VMD-L on correspondences so that everyone can benefit from the
> discussion.
>
> You have to change the offending entry in the parameter file that you
> are passing into NAMDEnergy.
>
> Regards,
> Christopher Mayne
>
> On Mar 30, 2015, at 11:34 AM, Subrata Paul wrote:
>
> Thanks Christopher,
>
> How can i change the periodicity in VMD NAMDenergy pluging
>
>
>
> On Mon, Mar 30, 2015 at 7:56 PM, Mayne, Christopher G <
> cmayne2_at_illinois.edu> wrote:
>
>> 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 *
>>
>>
>>
>
>
> --
>
>
>
>
>
> *With Best Regards Subrata Paul PhD Student Dept of Chemistry. IIT
> Guwahati *
>
>
> 

-- 
*With Best RegardsSubrata PaulPhD StudentDept of Chemistry.IIT Guwahati*