Just a guess:
Maybe just the atom-mask expression in the rms command is not
understandable to cpptraj as it contains a space between residue and
atom specification.
Instead of
.N,CA,C,O :76-112
try to use
:76-112.N,CA,C,O
Maybe that works.
(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.)
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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Received on Fri Jun 10 2016 - 01:30:03 PDT
