From: B Hartzoulakis (B.Hartzoulakis_at_Xention.com)
Date: Fri Jan 04 2013 - 05:14:29 CST
Hi All
I solved the problem mentioned below. For some reason my pdb file
(despite the fact that was generated following the general instruction
in the tutorial) was slightly different from the tutorial one.
1) Lipid definition to 'POPCL' - otherwise the membrane was not
defined correctly
2) I had to change the location where string3 was defined in the
TCL script (one column space difference than the one in the examples)
So when these were changed the script worked as expected.
Thanks
Basil
--------------------------------------------------------------
Basil Hartzoulakis, PhD
Principal Scientist
Xention Ltd
email: b.hartzoulakis_at_xention.com
linkedin: http://uk.linkedin.com/in/drugdesigner
Web: www.xention.com <http://www.xention.com/>
From: B Hartzoulakis
Sent: 03 January 2013 12:16
To: 'namd-l_at_ks.uiuc.edu'
Subject: Issues with the "Keep Water Out" tcl script
Hi
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
--------------------------------------------------------------
Basil Hartzoulakis, PhD
Principal Scientist
Xention Ltd
email: b.hartzoulakis_at_xention.com
linkedin: http://uk.linkedin.com/in/drugdesigner
ERROR LOG
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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