Thanks Jason
George
On May 9, 2011, at 9:17 PM, Jason Swails wrote:
> On Mon, May 9, 2011 at 8:48 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> 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)
>>
>
> Curly braces {}, not parentheses ()
>
>
>> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon May 09 2011 - 13:00:02 PDT
