Please upgrade to AmberTools 16: http://ambermd.org/AmberTools16-get.html
-Dan
On Thu, May 26, 2016 at 8:58 AM, colvin chin <colvin4367.gmail.com> wrote:
> Hi.
>
> No. This is the output from ver. 15...
>
>> On 26 May 2016, at 10:42 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> Hi,
>>
>>> On Thu, May 26, 2016 at 7:56 AM, colvin chin <colvin4367.gmail.com> wrote:
>>>
>>> I copied the wrong output for case 1. For case 1, I used rms reference, and the output didn't state the reference mask as in the output for case 2 when I use rms first. I did specified reference structure before the rms reference command. Am I missing anything here?
>>
>> Are you sure you are using the latest version of cpptraj (16)? I get
>> reference mask output whether I use 'first' or 'reference':
>>
>> ```
>> ACTION SETUP FOR PARM 'tz2.truncoct.parm7' (3 actions):
>> 0: [rms Res2-11 first :2-11 out rmsd.dat]
>> Target mask: [:2-11](182)
>> Reference mask: [:2-11](182)
>> Warning: Coordinates are being rotated and box coordinates are present.
>> Warning: Unit cell vectors are NOT rotated; imaging will not be possible
>> Warning: after the RMS-fit is performed.
>> 1: [rms Res2-11_mass reference :2-11 out rmsd.mass.dat mass]
>> Target mask: [:2-11](182)
>> Reference mask: [:2-11](182)
>> Warning: Coordinates are being rotated and box coordinates are present.
>> Warning: Unit cell vectors are NOT rotated; imaging will not be possible
>> Warning: after the RMS-fit is performed.
>> ```
>>
>> -Dan
>>
>>>
>>> Thanks!
>>>
>>>> On 26 May 2016, at 9:22 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>>
>>>> Hi,
>>>>
>>>>> On Thu, May 26, 2016 at 3:19 AM, colvin <colvin4367.gmail.com> wrote:
>>>>> Is this strange bug fixed?
>>>>>
>>>>> http://archive.ambermd.org/201509/0399.html
>>>>>
>>>>> I am still getting the same problem as described. Currently using CPPTRAJ ver. 15.
>>>>
>>>> That bug is indeed fixed in version 16 (and I recommend upgrading).
>>>> However, your problem does not appear to be the same one.
>>>>
>>>>>
>>>>> Does this means that in case 1, the rmsd calculation is not rmsfit to the reference structure? and in case 2, it is rmsfit into the first frame of the input trajectory instead of my reference structure - min2_worst.rst?
>>>>
>>>> In both cases you're specifying 'first', which means use the first
>>>> frame read in as the reference structure. You need to specify
>>>> 'reference' or 'ref <refname>' etc. if you want to use a specific
>>>> reference structure. See the manual for full details.
>>>>
>>>>>
>>>>> For the atomicfluct, if rms reference command put before atomicfluct, the calculation will rmsfit to the reference structure, right?
>>>>
>>>> Yes, that is what the 'rms' command does by default unless 'nofit' or
>>>> 'nomod' is specified.
>>>>
>>>> Hope this helps,
>>>>
>>>> -Dan
>>>>
>>>>>
>>>>> My input:
>>>>> trajin ../combine_traj/combine-every-10ps-production.nc
>>>>> center :1-400
>>>>> image familiar
>>>>> reference ../../min2_worst.rst
>>>>> rms reference
>>>>> atomicfluct out backbonermsfluct_all :1-400.C,CA,N,O byres
>>>>> atomicfluct out backbonermsfluct_all.arg :1-400.C,CA,N,O byres
>>>>> atomicfluct out backbonermsfluct_all.gnu :1-400.C,CA,N,O byres
>>>>> atomicfluct out backbonermsfluct_rec :1-394.C,CA,N,O byres
>>>>> atomicfluct out backbonermsfluct_rec.arg :1-394.C,CA,N,O byres
>>>>> atomicfluct out backbonermsfluct_rec.gnu :1-394.C,CA,N,O byres
>>>>> atomicfluct out backbonermsfluct_pep :395-400.C,CA,N,O byres
>>>>> atomicfluct out backbonermsfluct_pep.arg :395-400.C,CA,N,O byres
>>>>> atomicfluct out backbonermsfluct_pep.gnu :395-400.C,CA,N,O byres
>>>>> atomicfluct out backbonermsfluct_activesite :395-400<:4.0 byres
>>>>> go
>>>>>
>>>>> Pls advise.
>>>>>
>>>>> Thank you very much!!
>>>>> _______________________________________________
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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)
>>>>
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>>>
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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)
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
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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)
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Received on Thu May 26 2016 - 08:30:02 PDT
