Ah, thank you. Must've missed that.
On 16/10/2017 21:23, Daniel Roe wrote:
> Hi,
>
> From the Amber 17 manual, cpptraj 'vector' command section 28.9.79 (pg 644):
>
> "[out <filename>] Write vector data to <filename> with format ’Vx Vy
> Vz Ox Oy Oz’ where V denotes vector coordinates and ’O’ denotes origin
> coordinates."
>
> Hope this helps. Let me know if you have more questions.
>
> -Dan
>
> On Mon, Oct 16, 2017 at 12:14 AM, Pietro Aronica
> <pietroa.bii.a-star.edu.sg> wrote:
>> Hello,
>>
>> I am working with a lipid bilayer, and I am trying to look at analysis
>> commands in cpptraj to quantitatively examine my system. One of the
>> things I am trying to do is monitor the position of a guanidine group on
>> an arginine on an embedded peptide with respect to the hydrophilic heads
>> of the lipids. My first instinct was to simply calculate distances
>> between centres of mass but this method will show that distance is
>> increasing if the guaninide is still near the heads but off-centre,
>> which obviously not ideal.
>>
>> It was pointed out to me to use a vector command instead and use the
>> z-component to determine the position of the guanidine group, but I need
>> help interpreting the output. I used this command:
>>
>> vector mask out vector.dat .%N2 :49-192&:PC
>>
>> where @%N2 is to identify the guanidine group and :49-192&:PC the top
>> leaflet's hydrophilic heads.
>>
>> The output is six numbers (technically 7, the first being the frame),
>> and I am unsure what these represent. I think three are the vector
>> origin and three are the x, y and z components of the vector, but which
>> one is which? Is there something I am overlooking?
>>
>> I'm sorry if this sounds like a silly question but the manual does not
>> specify and I couldn't find a clear, unambiguous explanation.
>>
>> Also, if I am going about this lipid analysis wrong, do tell me.
>>
>> Kind regards
>>
>> Pietro
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Oct 16 2017 - 21:00:02 PDT
