I’m using CPPTRAJ: Trajectory Analysis. V17.00
I An analogous script for rmsd analysis works with the ‘ref’ keyword
parm complex_solv.modO.prmtop [CX]
parm subA.pdb [Xray]
trajin cmplx.pH_5.60ns.nc [CX]
reference subA.pdb parm [Xray]
rms ToXray ref [Xray] :10-125.CA :10-125.CA out rmsd.agr
George
> On 26 Sep 2017, at 18:46, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> What version of cpptraj are you using? The 'ref' keyword for
> 'distance' is currently only available in the GitHub version of
> cpptraj.
>
> -Dan
>
> On Tue, Sep 26, 2017 at 12:41 PM, George Tzotzos <gtzotzos.me.com> wrote:
>> I’m trying to compute the distance between the centres of mass of two helices using a PDB file as reference.
>> My input file is:
>>
>> parm complex_solv.modO.prmtop
>> parm subA.pdb [Xray]
>> trajin cmplx.pH_5.60ns.nc
>> reference subA.pdb parm [Xray]
>> distance ToXray ref [Xray] :103-117.CA :82-92.CA out DIST.agr
>> run
>>
>> I get the following error:
>>
>> [distance ToXray ref [Xray] :103-117.CA :82-92.CA out DIST.agr]
>> DISTANCE: :103-117.CA to :82-92.CA, center of mass.
>> Error: [distance] Not all arguments handled: [ ref [Xray] ]
>>
>>
>> I thought the first mask refers to the reference and the second to the trajectory. I’d be grateful for any suggestions regarding these errors.
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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
>
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Received on Tue Sep 26 2017 - 10:30:02 PDT
