From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Mon Nov 26 2018 - 09:26:06 CST

Dear Lorenzo,

I am assuming that you are referring to the simulation executed using the
configuration file kcsa_popcwimineq-02.conf, is that correct? The error
seems to occur because, for some reason, the atoms were not properly
defined in the pdb that the script is loading. For this case, and for any
occasion that you have a script that is dealing with reading and setting
atom's properties, I would suggest you to debug the script using a few
"puts" statements to extract the value of the variables at different stages
of the execution. For instances, add the line 'puts atomid $segname $resid
$atom"' after the line 126, before the problematic command and check which
atoms the command is getting. Then check if the atom exists in the pdb that
you are loading in the script, containing the exact same information:
segname resid and atom's name.

I tested the simulation with the files provided in the tutorial-files
folder and the simulation had no issue in that particular command.

Best

João

On Sat, Nov 24, 2018 at 2:38 AM Lorenzo Fabbri <
lorenzo.fabbri-1_at_studenti.unitn.it> wrote:

> 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.
>

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851
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