Glad to hear it's working now. Still, the current behavior is not
ideal and I'm currently working on a fix. Thanks again for the report,
-Dan
On Mon, Sep 28, 2015 at 6:57 AM, Chris <dlutlife223.163.com> wrote:
> Dear Dan
>
> Thanks for your reply and sorry for my belatedreply.
> I tried your code and it works.
> It seems like I should do a meaningless command before rms command.
>
> Chris
>
>
>
>
>
>
>
>
>
> At 2015-09-24 23:19:47, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>>OK, it is a strange bug and I won't bore you with the details but you
>>can work around this issue by forcing cpptraj to set the active
>>reference like so:
>>
>># Step 1. Force cpptraj to set active reference for topology.
>># Only load 1 trajectory frame.
>>parm pro_com.prmtop
>>reference wat_box.inpcrd [R0]
>>trajin ../traj/md1.nc 1 1
>># Blank action
>>unstrip
>>run
>>clear trajin
>># Step 2. Now read in entire traj.
>>trajin ../traj/md1.nc
>># Create another reference, [R1]. This one will work with distance based masks.
>>reference wat_box.inpcrd [R1]
>># Now execute rms command
>>rmsd rms_test :250<:10&.CA,N,C ref [R1] out rms_test.dat time 0.002
>>
>>Try it and let me know if it works. Thanks for the report.
>>
>>-Dan
>>
>>
>>On Thu, Sep 24, 2015 at 8:55 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>> Seems like it might be a bug. I'll look into it.
>>>
>>> -Dan
>>>
>>> On Thu, Sep 24, 2015 at 6:46 AM, Chris <dlutlife223.163.com> wrote:
>>>> Dear Jason:
>>>> Thanks for your concern!
>>>> cpptraj version is 15:
>>>> cpptraj -V: CPPTRAJ: Version V15.00
>>>>
>>>> command:
>>>> rmsd rms_test :250<:10&.CA,N,C reference out rms_test.dat time 0.002 ,
>>>>
>>>> when key world "reference" replaced by "first" could goes well, but I have already define a reference before.
>>>> Thank you for check weather it is a bug or just I AM WRONG!
>>>>
>>>> Best
>>>> Chris
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> At 2015-09-22 20:15:26, "Jason Swails" <jason.swails.gmail.com> wrote:
>>>>>On Tue, Sep 22, 2015 at 12:01 AM, Chris <dlutlife223.163.com> wrote:
>>>>>
>>>>>> Hi, Dear All!
>>>>>>
>>>>>> I want to calculated RMSD around a residue ( 10A nearby)
>>>>>> According to manual. The command I am using in cpptraj:
>>>>>>
>>>>>> parm pro_com.prmtop
>>>>>> reference wat_box.inpcrd
>>>>>> trajin ../traj/md1.nc
>>>>>> rmsd rms_test :250<:10&.CA,N,C reference out rms_test.dat time 0.002
>>>>>>
>>>>>> But it occurs error:
>>>>>>
>>>>>> Error: No reference set for [pro_com.prmtop], cannot select by distance
>>>>>> Error: Could not initialize action [rmsd]
>>>>>>
>>>>>> BUT, when I change code to:
>>>>>> rmsd rms_test :250<:10&.CA,N,C first out rms_test.dat time 0.002
>>>>>>
>>>>>> It goes well, But it is not I want.
>>>>>>
>>>>>> Anyone can explain this to me?
>>>>>>
>>>>>
>>>>>What version of cpptraj are you using? (It should say the version in the
>>>>>header of the program output).
>>>>>
>>>>>All the best,
>>>>>Jason
>>>>>
>>>>>--
>>>>>Jason M. Swails
>>>>>BioMaPS,
>>>>>Rutgers University
>>>>>Postdoctoral Researcher
>>>>>_______________________________________________
>>>>>AMBER mailing list
>>>>>AMBER.ambermd.org
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>>>> _______________________________________________
>>>> AMBER mailing list
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe, PhD
>>> Department of Medicinal Chemistry
>>> University of Utah
>>> 30 South 2000 East, Room 307
>>> Salt Lake City, UT 84112-5820
>>> http://home.chpc.utah.edu/~cheatham/
>>> (801) 587-9652
>>> (801) 585-6208 (Fax)
>>
>>
>>
>>--
>>-------------------------
>>Daniel R. Roe, PhD
>>Department of Medicinal Chemistry
>>University of Utah
>>30 South 2000 East, Room 307
>>Salt Lake City, UT 84112-5820
>>http://home.chpc.utah.edu/~cheatham/
>>(801) 587-9652
>>(801) 585-6208 (Fax)
>>
>>_______________________________________________
>>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, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
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Received on Mon Sep 28 2015 - 08:30:03 PDT
