Issues with the "Keep Water Out" tcl script

From: B Hartzoulakis (
Date: Thu Jan 03 2013 - 06:15:50 CST


And thanks in advance for your help. I applied the membrane protein
tutorial (written for the Kcsa Ion channel) to a recently published
structure of sodium channel (4f4l). I had to change several scripts and
adapt them for the new channel but everything worked more or less
according to the tutorial so I completed the first step of melting the
lipid side chains successfully.


Unfortunately when I tried to use the keep_water_out.tlc script I get a
simulation termination with the lines from the error log

(see text at the end of my message). I have done the following


1) I checked the corresponding pdb/psf files in the tutorial and in
my files and I cannot see any problems/differences with waters
definitions or residue names to justify this problem

2) I run the problematic part of the "keep water out tcl" scrip
line by line for the system in question and I get the same error message
when the building of the water indices list is taking place. The
interesting thing I do not understand is that the script runs fine for
the kcsa (as in the tutorial) but when I tried it line by line against
the kcsa I get again the same error.


All my files are in a DropBox folder, so if interested to help me I can
share the link with you.


Thanks again




Basil Hartzoulakis, PhD

Principal Scientist

Xention Ltd

email: <>






Charm++: standalone mode (not using charmrun)

Charm++ warning> fences and atomic operations not available in native

Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21

[0] isomalloc.c> Disabling isomalloc because mmap() does not work

CharmLB> Load balancer assumes all CPUs are same.

Charm++> Running on 1 unique compute nodes (8-way SMP).

Charm++> cpu topology info is gathered in 0.106 seconds.

Info: NAMD 2.9 for Win32-multicore






TCL: Starting Tcl forces

TCL: atom not found

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)


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