The 'ref' keyword for 'rmsd' has been supported for years. The 'ref'
keyword for distance was only recently added (after the release of
AT17): https://github.com/Amber-MD/cpptraj/pull/510
In order to use the 'ref' keyword with 'distance' you will have to use
the GitHub version.
-Dan
On Tue, Sep 26, 2017 at 1:02 PM, George Tzotzos <gtzotzos.me.com> wrote:
> 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.
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> 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
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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
