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From: hamze rahimi (buksanbio_at_gmail.com)
Date: Fri Nov 04 2011 - 04:30:38 CDT
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Dear expert
I have about 15 dcd files. these files are really huge files! each of them
is about 100 GB, therefore I must use bigdcd for analysis such files.
now set under script but this has problem with bigdcd arguments:
""
proc avStruct {selStr start stop fName {molid top}} {
set sel [atomselect ${MOL} $selStr]
set avXYZ [measure avpos $sel first $start last $stop]
set xyzBak [$sel get {x y z}]
$sel set {x y z} $avXYZ
$sel writepdb ${fName}.pdb
$sel set {x y z} $xyzBak
$sel delete
}
set MOL
animate read pdb ${MOL}_ionized.pdb
bigdcd myavStruct ${MOL}_eq.dcd
""
my error :
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Info) Using plugin dcd for coordinates from file fgf80_eq.dcd
bigdcd aborting at frame 1
invalid command name "myavStruct"
bigdcd_done
Thanks a lot for any suggestion or idea
best wishes
-- Hamzeh Rahimi PhD student in Medical Biotechnology Pasteur institute Tel:+989125975321
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