Thanks Jason
I tried your suggestion. I'm copying from terminal:
> COMPLEX=loadpdb 2wc6_bom.pdb
Loading PDB file: ./2wc6_bom.pdb
total atoms in file: 2256
> set COMPLEX box (67.602 60.679 66.072)
set: Improper number of arguments!
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
ERROR: syntax error
Cheers
George
On May 9, 2011, at 8:04 PM, Jason Swails wrote:
> Hello,
>
> On Mon, May 9, 2011 at 8:00 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Hi everybody,
>>
>> I'm dealing with a modified trajectory file (have stripped HOHs from the
>> original file). I need to generate a new topology file for my complex.
>>
>> I load my complex in tleap
>>
>>> COMPLEX = my_complex.pdb
>>
>
> Do you mean
>
> COMPLEX = loadpdb my_complex.pdb
>
> ?
>
>
>
>>
>> Then I try to set a unit box using the box dimensions taken from the
>> modified trajectory file (last line).
>>
>> I do a
>>
>>> set COMPLEX box 67.602 60.679 66.072
>>
>> and get
>>
>> set: Improper number of arguments!
>> usage: set <container> <parameter> <object>
>> or: set default <parameter> <value>
>>
>
> This means you can only have 1 value. Thus, the box dimensions must be an
> array (I would guess). Try
>
> set COMPLEX box {67.602 60.679 66.072}
>
> HTH,
> Jason
>
>
>>
>>
>> I'd appreciate your suggestions on the correct syntax for setting the unit
>> box.
>>
>> Many thanks in advance
>>
>> George
>>
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>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Mon May 09 2011 - 12:00:03 PDT
