VMD-L Mailing List

From: Eduard Schreiner (eschrein_at_ks.uiuc.edu)
Date: Tue Jan 04 2011 - 07:48:33 CST

you should check, which of your set calls generates the error. I just
tried the code you provided with some other files and is worked. So
the problem seems to be related to your specific case.

eddi

On Tue, Jan 4, 2011 at 7:37 AM, <pragya.saxena_at_research.iiit.ac.in> wrote:
> I am getting the following error
>
> wrong # args: should be "set varName ?newValue?"
>
>
> ----- Original Message -----
> From: "Eduard Schreiner" <eduard.schreiner_at_gmail.com>
> To: "pragya saxena" <pragya.saxena_at_research.iiit.ac.in>
> Cc: vmd-l_at_ks.uiuc.edu
> Sent: Tuesday, January 4, 2011 5:01:58 PM
> Subject: Re: vmd-l: Regarding fitframes.tcl
>
> but you do not change the selection in the animate write command;
> check the manual for the usage of animate write. Try:
>
> animate write dcd fitted_all2.dcd beg 1 end $fin waitfor all sel
> [atomselect top "protein and not resname MTX"]
>
>
> eddi
>
> On Tue, Jan 4, 2011 at 4:51 AM,  <pragya.saxena_at_research.iiit.ac.in> wrote:
>> Hi,
>>
>> I am using fitframes.tcl to write a dcd file for only protein (Dihydrofolate reductase-methotrexate---DHFR-MTX).
>>
>> ## This takes a selection and fits that selection for every frame in the
>> ## molecule (all atoms are moved, but the fit is based on the selection).
>> ##
>> ## For example:  fitframes top "protein"
>> ##
>> ## -Jim
>> set molid top
>> set seltext protein
>> mol load pdb ionized.pdb dcd md03_traj.dcd
>>  set ref [atomselect $molid $seltext frame 1]
>>  set sel [atomselect $molid $seltext]
>>  set all [atomselect $molid all]
>>  set n [molinfo $molid get numframes]
>>  set fin [expr $n-1]
>>
>>  for { set i 1 } { $i < $n } { incr i } {
>>    $sel frame $i
>>    $all frame $i
>>    $all move [measure fit $sel $ref]
>>  }
>> animate write dcd fitted_all2.dcd beg 1 end $fin waitfor all sel [atomselect top protein]
>>
>>
>> However in the resultant dcd file, the cordinates for drug(MTX) are also coming..
>> Following is the drug in the pdb file that I am using
>>
>> ATOM   2490  N1  MTX O 161      32.399  40.535  11.719  1.00  0.00      O1   N
>>
>> I have tried various selections for seltext variable like:-
>> protein and not resname MTX
>> protein and not resid 161
>> protein and not MTX
>> segid P1 #(for protein)
>>
>> I want to know where I am going wrong and what should be done.
>> Kindly help.
>>
>> Thanks and Regards
>> Pragya Saxena
>>
>
>
>
> --
> --
>
> =============================================================================
> Eduard Schreiner
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
> Phone: 217-244-4361
> Fax: 217-244-6078
> http://www.ks.uiuc.edu/~eschrein/
> =============================================================================
> 

-- 
--
=============================================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
=============================================================================