From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Apr 11 2017 - 22:16:52 CDT

Dear Jrhau,
Are you certain that you used all of the same parameter files as in your simulation? If so, can you send the namdenergy config file generated by running with the debug box checked?
Thanks,
Peter

> On Apr 11, 2017, at 9:03 PM, jrhau lung <jrhaulung_at_gmail.com> wrote:
>
> Dear VMD friends:
> After finishing a simulation, I would like to analyze the nonbond energy between my substrate and enzyme. After uploading the psf and dcd in vmd main and setup parameters in NAMD ENERGY plugin, including input parameter in selection and uploading xsc result from simulating result, etc. and hit rung bottom. I got the following error message and need some help to get through. Thanks!
>
> sincerely,
>
> Jrhau
>
>
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB1
>
> Charm++ fatal error:
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB1
>
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB1
>
> Charm++ fatal error:
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB1
>
> while executing
> "exec $namdcmd ${jobname}-temp.namd > ${jobname}-temp.log"
> (procedure "namdrun" line 56)
> 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)