VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 04 2011 - 07:29:32 CDT

On Nov 4, 2011, at 6:42 AM, hamze rahimi <buksanbio_at_gmail.com> wrote:

>
> 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:

You have more problems than that. Almost nothing about the script code
you quote makes any sense. It is not clear what you are trying to do,
but please note that just guessing some random modifications to a
script will make it work. You first have to learn how to write script
code in Tcl and it's VMD extensions before you have a chance of being
successful.
There ain't no such thing as a free lunch...

Axel

> ""
> 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
>