Tutorial-l Mailing List

From: Kevin KNOOPS (keknoops_at_embl.fr)
Date: Tue Aug 10 2010 - 10:05:21 CDT

Dear all,

I am trying to follow the membrane protein tutorial and till now (page
40, step 9), it has been very informative. However, when I am trying to
run the second NAMD2 command, I keep getting the same message:

bash-3.2$ namd2 kcsa_popcwimineq-02.conf > kcsa_popcwimineq-02.log
------------- 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 124)

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 124)

Aborted
bash-3.2$

Would somebody have a suggestion how to continue?? Thank you in advance!

Kind regards from Grenoble,

Kevin Knoops
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