From: Edelmiro Moman (edelmiro.moman_at_gmail.com)
Date: Tue Mar 02 2010 - 13:53:08 CST

I would be great if you let us know...

On Tue, Mar 2, 2010 at 7:33 PM, Bernardo Sosa Padilla Araujo
<bernardospa_at_gmail.com> wrote:
> Never mind. I found out what the problem was.
>
>
>
> 2010/3/1 Bernardo Sosa Padilla Araujo <bernardospa_at_gmail.com>
>>
>> Hi all,
>>
>> I am trying to write a script to measure the distance between a few atoms
>> for a simulation and write that in a file.
>> Here is my script:
>>
>> =================================================
>> #opening files to write
>> set dist1 [open dist1.dat w]
>> set dist2 [open dist2.dat w]
>> #getting number of frames
>> set nf [molinfo top get numframes]
>> #selecting the atoms
>> set sub [atomselect top "name H4"]
>> set base1 [atomselect top "name OE1 and within 6 of name H4"]
>> set base2 [atomselect top "name OE2 and within 6 of name H4"]
>> #creating variables with the index from the previous selection
>> set hydr [$sub get index]
>> set ox1 [$base1 get index]
>> set ox2 [$base2 get index]
>> #outputting the measurements
>> set a {}
>> set b {}
>> for { set i 0} { $i <=$nf } {incr i} {
>>  lappend a [measure bond {$ox1 $hydr} frame $i]
>>  lappend b [measure bond {$ox2 $hydr} frame $i]
>> }
>> puts $dist1 "$a"
>> close $dist1
>> puts $dist2 "$b"
>> close $dist2
>> =================================================
>>
>> So, I select three atoms and then from those selections I create 3
>> different variables (hydr, ox1 and ox2) that hold the indexes for the three
>> atoms(red text).
>> Then I use the measure command to measure the distances between the
>> atoms(green text).
>> The measure command should be used:
>> measure bond {atomid1 atomid2}    ex : measure bond {3 5}
>> What I am doing is to put the name of the variable that holds the atomids
>> instead of putting the number. And it is not working at all, it gives this
>> error message "expected integer but got $ox1 measure bond: bad atom index".
>> But when I put the numbers (instead of the name of the variables that hold
>> the numbers) it works just fine.
>> Then my question is if you see any mistake in the script that could be
>> producing this error or if anyone knows of a different way to do it.
>>  Thanks a lot in advance.
>>
>> Bernardo
>>
>>
>
>

-- 
Edelmiro Moman, PhD
ProSciens, Computing & Molecular Sciences
2 rue du Palais de Justice
L-1841 Luxembourg
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E-mail: edelmiro.moman_at_gmail.com
E-mail: moman_at_prosciens.com
Website: http://www.edelmiromoman.eu/
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