RE: Issues with the "Keep Water Out" tcl script

Date: Thu Jan 03 2013 - 09:09:29 CST



If I remember correctly the keep_water_out.tcl script contained a few exceptions for atom indices to keep in the beginning of the script. These are for sure different in your simulation, did you adapt (or erase) them accordingly? It's the definition of the watexcept variable I am talking about (line 56). Another problem could be the residue name of your water defined in your PSF and the tcl script, are they called the same in both cases? Same for the atom name of the water (OH2 in my case considering only the oxygen).


Anyway, just guessing here, the VMD people might be of better help there ;)


Best regards.




De : [] De la part de B Hartzoulakis
Envoyé : jeudi 3 janvier 2013 13:16
À :
Objet : namd-l: Issues with the "Keep Water Out" tcl script



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







Charm++: standalone mode (not using charmrun)

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

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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