VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Nov 04 2011 - 06:03:16 CDT

As the error message clearly states:
there is no command named myavStruct, since you named it avStruct.
 I'm also not sure off the top of my head, what parameters a proc for
bigdcd can take. I think it only takes a frame number, the rest you have to
pass as global variables. See the documentation for bigdcd.tcl.

-Ajasja

On Fri, Nov 4, 2011 at 10:30, 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:
> ""
> 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
>
>