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
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>
>
>
> --
> -------------------------
> 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)
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Received on Thu Sep 24 2015 - 08:30:02 PDT
