The manual doesn’t say that v1, v2 are masks. That was my erroneous interpretation.
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
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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Received on Wed Oct 04 2017 - 10:00:04 PDT
