From: Bjørnar Jensen (bje076_at_ift.uib.no)
Date: Fri Sep 28 2012 - 08:39:04 CDT

Hello again!

Well, I do have another suggestion:

On the page:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/
you can see several examples of how to use bigdcd.

It seems like you're passing the wrong function into bigdcd.

The syntax should be "bigdcd procedure_to_run file_type filename".
You're passing in
the "measure" command without any parameters, while you should be
passing in
your gyration procedure.

So the line should be: bigdcd gyration dcd CALDHmT178_wb_eq5.dcd

Best of luck,
Bjørnar.

On 2012-09-28 15:07, flavio seixas wrote:
>
> Hi Joaquim and Bjornar,
>
> Thanks for your advices.
>
> I tried to incorporate your suggestions but the script still not
> working properly.
>
> Any other suggestions?
>
>
> proc gyration { frame } {
> global ref sel all outfile
> $all move [measure fit $ref $sel]
> puts "$frame: [measure rgyr $sel]"
> puts $outfile "[measure rgyr $sel]"
> }
> set mol [mol addfile CALDHmT178_wb_min4.coor type pdb waitfor all]
> set all [atomselect $mol all]
> set ref [atomselect $mol "protein and backbone and noh" frame 1]
> set sel [atomselect $mol "protein and backbone and noh"]
> set outfile [open gyration.dat w]
> bigdcd measure dcd CALDHmT178_wb_eq5.dcd
> bigdcd_wait
> close $outfile
>
>
>
> --- On *Fri, 9/28/12, Bjørnar Jensen /<bje076_at_ift.uib.no>/* wrote:
>
>
> From: Bjørnar Jensen <bje076_at_ift.uib.no>
> Subject: Re: vmd-l: Radius of gyration from Big DCD
> To: "flavio seixas" <oivalf_nix_at_yahoo.com>
> Cc: "VMD List" <vmd-l_at_ks.uiuc.edu>
> Date: Friday, September 28, 2012, 11:35 AM
>
> Hello,
>
> while it may or may not solve your problem, there seems to be an
> error in your script
> related to the [measure rgyr] command.
>
> According to the user manual:
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node136.html
> *rgyr /selection/ [weight /weights/]*: Returns the radius of
> gyration of atoms in /selection/ using the given weight.
>
> Note how this command only accept ONE selection, while your use of
> the command is:
>
> [measure rgyr $sel $ref]
>
> ,where you're using two selections.
>
> When using the measure command in your manner in the TkConsole, I get:
>
> 55 % measure rgyr $sel $sel2
> wrong # args: should be "measure rgyr <selection> [weight <weights>]"
>
> Basically, you're not getting any data in your file as the script
> aborts whenever it reaches this command.
>
>
> Best regards,
> Bjørnar
>
> On 2012-09-27 21:08, flavio seixas wrote:
>> Hi,
>>
>> I based in the Tcl tutorial onwww.tcl.tk <http://www.tcl.tk> as well vmd-list to make the script below aiming to calculate the gyration radius over simulation time from a BigDCD file.
>>
>> proc gyration { frame } {
>> global ref sel all outfile
>> $all move [measure fit $sel $ref]
>> puts "$frame: [measure rgyr $sel $ref]"
>> puts $outfile "[measure rgyr $sel $ref]"
>> }
>> set mol [mol addfile CALDHmT178_wb_min4.coor type pdb waitfor all]
>> set all [atomselect $mol all]
>> set ref [atomselect $mol "protein and backbone and noh" frame 0]
>> set sel [atomselect $mol "protein and backbone and noh"]
>> set outfile [open gyration.dat w]
>> bigdcd measure dcd CALDHmT178_wb_eq5.dcd
>> bigdcd_wait
>> close $outfile
>>
>>
>> However, after running there is nothing on output file gyration.dat
>>
>> I am not a developer, just an user
>> and I am not able to find the error.
>>
>> Does someone could give me a clue about what is missing in the script above?
>>
>> Thanks for any help.
>>
>> Flavio
>>
>>
>>
>>
>