On Fri, Jun 10, 2016 at 2:21 AM, Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> (I just checked the Amber16 manual for the Amber mask explanation; there
> are only 'pure' sample cases given like :1-10 or :LYS or .C,CA,N or
> .%CT, but no 'mixed' cases like :1-10.CA.)
In the cpptraj section of the manual, 29.2.2 "Atom Mask Selection
Syntax", there are many example mask expressions given, including
several compound expressions.
-Dan
>
> Regards,
>
> Anselm
>
>
> Am 09.06.2016 21:47, schrieb Hai Nguyen:
>> On Thu, Jun 9, 2016 at 3:40 PM, Aishani Prem <aishaniprem.gmail.com> wrote:
>>
>>> The command goes like:
>>> $AMBERHOME/bin/cpptraj -p pdb_vac.prmtop -i rmsd_cpptraj.trajin
>>>> cpptraj.log
>>>
>>>
>> you throw all the log output to cpptraj.log.
>>
>> Hai
>>
>>
>>> On Thu, Jun 9, 2016 at 12:33 PM, Daniel Roe <daniel.r.roe.gmail.com>
>>> wrote:
>>>
>>>> Strange. How are you executing cpptraj (exact command on the command
>>> line)?
>>>>
>>>> Also, I recommend updating to AmberTools 16 if possible.
>>>>
>>>> -Dan
>>>>
>>>> On Thu, Jun 9, 2016 at 1:31 PM, Aishani Prem <aishaniprem.gmail.com>
>>>> wrote:
>>>>> It wont throw me an output file or an error, and the version I am using
>>>> is
>>>>> V15.00
>>>>>
>>>>> On Thu, Jun 9, 2016 at 12:17 PM, Daniel Roe <daniel.r.roe.gmail.com>
>>>> wrote:
>>>>>
>>>>>> Can you please post your entire cpptraj output? Also, what version of
>>>>>> cpptraj are you using?
>>>>>>
>>>>>> -Dan
>>>>>>
>>>>>> On Thu, Jun 9, 2016 at 1:14 PM, Aishani Prem <aishaniprem.gmail.com>
>>>>>> wrote:
>>>>>>> Hi,
>>>>>>> I am trying to get the RMSD of the backbone atoms for a
>>> specific
>>>>>> set
>>>>>>> of residues in my simulations. My input file looks like:
>>>>>>> trajin pdb_nocut.mdcrd
>>>>>>> reference pdb_nocut.rst
>>>>>>> autoimage
>>>>>>> rms reference mass out pdb_backbone_nocut_cpptraj.rms .N,CA,C,O
>>>> :76-112
>>>>>>> time 0.1
>>>>>>>
>>>>>>> When I run this , I dont get any error but my output file is not
>>>>>> generated
>>>>>>> either. Am I doing anything wrong?
>>>>>>> --
>>>>>>> Thank You and Regards,
>>>>>>> Aishani Chittoor Prem
>>>>>>> _______________________________________________
>>>>>>> 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)
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Thank You and Regards,
>>>>> Aishani Chittoor Prem
>>>>> _______________________________________________
>>>>> 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)
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>> --
>>> Thank You and Regards,
>>> Aishani Chittoor Prem
>>> _______________________________________________
>>> 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
>>
>>
>
>
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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)
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Received on Fri Jun 10 2016 - 08:00:03 PDT
