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
>>>>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)
>
>
>
>--
>-------------------------
>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
Received on Mon Sep 28 2015 - 06:00:05 PDT
