From: Pete Kekenes-Huskey (huskeypm_at_gmail.com)
Date: Tue Sep 06 2011 - 17:22:26 CDT
Dear all,
Has anyone encountered the error "Modification of non-creatable array
values attempted" while running namd2_ti.pl?
I have ran a series of TI calculations for the alchemical
transformation for a single point mutation of a protein. The
transformation was partitioned into twenty steps, each having 250000
steps of equilibration and another 250K steps for statistics, using
commands like this:
alch On
alchType ti
alchVdwLambdaEnd 0.5
alchFile $inputname.fep
alchCol O
alchOutfile $outputname.tiout
alchVdWShiftCoeff 6 # Enable soft-core vdW potential
alchElecLambdaStart 0.5 #
alchOutFreq 5
alchEquilSteps 250000
set Lambda 0.01
set Ival 0.05
alchLambda $Lambda
set Lambda2 [expr $Lambda +$Ival]
alchLambda2 $Lambda2
run 500000
I ran these files with the NAMD_2.7b4_Linux-x86_64 executable, the
jobs completed without error and the *tiout outputs seem to be
reasonable. When running namd2_ti.pl (obtained from
http://www.ks.uiuc.edu/Research/namd/utilities/), I receive the
following error:
Ranger (E40A): ~/bin/namd2_ti.pl *tiout
Found 20 output files
Reading files: ....Modification of non-creatable array value
attempted, subscript -49999 at
/share/home/00623/tg457915/bin/namd2_ti.pl line 102, <FILE> line
50009.
Repeating the protocol for the files corresponding to lambda values
0..0.5 work fine, but files corresponding to lambda>0.55 fail with
this error. Any clues?
Thanks in advance for your help
Pete
-- ====================== Peter Kekenes-Huskey, Ph.D. Postdoctoral Researcher UCSD Dept of Pharmacology 4205 Urey Hall 9500 Gilman Avenue La Jolla, CA 92093 ======================
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