Tutorial-l Mailing List

From: Lorenzo Fabbri (lorenzo.fabbri-1_at_studenti.unitn.it)
Date: Sat Nov 24 2018 - 02:38:08 CST

I’m trying to go over the Membrane Proteins tutorial but I’m having some difficulties with Section 3.2 (Minimization and Equilibration with Protein Constrained), specifically I get this error message:

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: atom not found
    while executing
"atomid $segname $resid $atom"
    ("foreach" body line 3)
    invoked from within
"foreach atomrecord $waters_list {
    foreach {segname resid atom} $atomrecord { break }
    set atomindex [atomid $segname $resid $atom]
    set fla..."
    (file "keep_water_out.tcl" line 125)

Charm++ fatal error:
FATAL ERROR: atom not found
    while executing
"atomid $segname $resid $atom"
    ("foreach" body line 3)
    invoked from within
"foreach atomrecord $waters_list {
    foreach {segname resid atom} $atomrecord { break }
    set atomindex [atomid $segname $resid $atom]
    set fla..."
    (file "keep_water_out.tcl" line 125)

 I modified the tcl script keep_water_out but I keep getting this message no matter what I do. I’m using NAMD 2.12 Linux-x86_64-multicore-CUDA.
**
** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
**