From: B Hartzoulakis (B.Hartzoulakis_at_Xention.com)
Date: Thu Jan 03 2013 - 06:15:50 CST
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 <mailto:b.hartzoulakis_at_xention.com>
linkedin: http://uk.linkedin.com/in/drugdesigner
<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)
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:20:50 CST