Tutorial-l Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Aug 12 2010 - 00:00:55 CDT

I guess something is wrong with your PDB file? Using the example output
provided, it works fine for me.

-----Original Message-----
From: owner-tutorial-l_at_ks.uiuc.edu [mailto:owner-tutorial-l_at_ks.uiuc.edu] On
Behalf Of Kevin KNOOPS
Sent: Tuesday, August 10, 2010 10:05 AM
To: tutorial-l_at_ks.uiuc.edu
Subject: tutorial-l: membrane protein tutorial

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
**
** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
**

**
** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
**