# Re: [AMBER] Vector math: a couple of questions

From: George Tzotzos <gtzotzos.me.com>
Date: Wed, 04 Oct 2017 18:56:04 +0200

Indeed it helps a lot.

Grateful for the clarification

George

> On 4 Oct 2017, at 18:54, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> On Wed, Oct 4, 2017 at 12:43 PM, George Tzotzos <gtzotzos.me.com> wrote:
>> If I want to calculate angle deviations from a specific reference structure can I set up the reference first e.g.
>>
>> reference X-ray.pdb parm X-ray.pdb [A]
>>
>> and then use
>>
>> vectormath reference [A] vec1 VA vec2 VB out vec.dat dotangle
>
> Not exactly. What you would first do is calculate the vector from the
> reference using 'crdaction' (since a reference is just really a COORDS
> data set):
>
> reference ref.pdb [A]
> crdaction [A] vector VA <vector keywords>
>
> Then you can calculate your vector from whatever trajectory:
>
> trajin mytraj.nc
> vector VB <vector keywords>
> vectormath vec1 VA vec2 VB <vectormath keywords>
>
> Hope this helps,
>
> -Dan
>
>
>>
>> Many thanks for your help
>>
>> George
>>
>>> On 4 Oct 2017, at 18:30, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>
>>> Hi,
>>>
>>> On Tue, Oct 3, 2017 at 2:42 PM, George Tzotzos <gtzotzos.me.com <mailto:gtzotzos.me.com>> wrote:
>>>> vectormath vec1 v1 vec2 v2 dotangle out dotproduct.dat name acos(|V1|*|V2|)
>>>>
>>>> Where v1 and v2 are masks of the type :res_start-res_end
>>>
>>> The 'vec1' and 'vec2' keywords are for specifying previously
>>> calculated or read in vector data sets. So you could for example
>>> create the vector data beforehand with the 'vector' command:
>>>
>>> vector VA :1 :10
>>> vector VB :11 :20
>>> vectormath vec1 VA vec2 VB out vec.dat dotangle
>>>
>>> Hope this helps,
>>>
>>> -Dan
>>>
>>> PS - Out of curiosity, where does it say that v1 and v2 should be
>>> masks? That's incorrect and I need to fix it.
>>>
>>>>
>>>> I’d like to use the corresponding vectors of an X-ray structure as a reference doing something. I’ve tried various permutations using something like
>>>>
>>>> parm solv.prmtop
>>>> parm X-ray.pdb
>>>> trajin traj.nc
>>>> reference X-ray.pdb parm X-ray.pdb [A]
>>>>
>>>> and then vectormath to no avail.
>>>>
>>>> I’d be grateful for any suggestions
>>>>
>>>> George
>>>>
>>>>
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>>>
>>>
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe
>>> Laboratory of Computational Biology
>>> National Institutes of Health, NHLBI
>>> 5635 Fishers Ln, Rm T900
>>> Rockville MD, 20852
>>> https://www.lobos.nih.gov/lcb <https://www.lobos.nih.gov/lcb>
>>>
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>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
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Received on Wed Oct 04 2017 - 10:00:06 PDT
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