You should use cpptrraj. ptraj is deprecated.
Hai
> On Dec 15, 2016, at 4:54 AM, Mary Varughese <maryvj1985.gmail.com> wrote:
>
> Hi,
>
>
> Is there any command corresponding to 'info' in ptraj ?
>
> I am more familiarized with ptraj than cpptraj.
>
>
> Thanking you
>
> mary
>
>> On 12/15/16, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>> The file written by 'out' will contain the cluster number for each frame.
>> In addition, the file written by 'info' will contain parseable text
>> representations of each cluster.
>>
>> -Dan
>>
>> On Wed, Dec 14, 2016 at 5:34 AM Mary Varughese <maryvj1985.gmail.com>
>> wrote:
>>
>>> Sir,
>>>
>>> I tried clustering in ptraj and it worked ok.
>>>
>>> When i tried to do mmpbsa.pl on the trajectory generated; snapshots
>>> are generating but on performing pbsa and nmode calculations, pbsa
>>> finishes giving huge negative values (7 or 9 digits) and nmode fails
>>> to run. Problems on missing bonds errors are also in the log file.
>>>
>>> Is there any other way to know which frames are included in each
>>> cluster (i could create snaphots if i know the frame numbers) or
>>> generate proper trajectory (manual says trajectory generated is in
>>> amber format by default).?
>>>
>>>
>>> Thanking you
>>>
>>> mary
>>>
>>>
>>>> On 12/7/16, Mary Varughese <maryvj1985.gmail.com> wrote:
>>>> Ok.
>>>>
>>>> Thank you sir
>>>> I wil try this.
>>>>
>>>> On Wed, Dec 7, 2016 at 1:39 AM, Daniel Roe <daniel.r.roe.gmail.com>
>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> This is almost right, but what you want to do is RMS-fit the DNA
>>>>> _before_ you cluster, then cluster on your ligand using 'nofit'. So
>>>>> something like:
>>>>>
>>>>> parm myparm.parm7
>>>>> trajin mytraj.nc
>>>>> rms first <DNA backbone mask>
>>>>> cluster <ligand mask> nofit ...
>>>>>
>>>>> Hope this helps,
>>>>>
>>>>> -Dan
>>>>>
>>>>> On Thu, Dec 1, 2016 at 5:43 AM, Mary Varughese <maryvj1985.gmail.com>
>>>>> wrote:
>>>>>> Sir
>>>>>>
>>>>>> Thank you very much.
>>>>>>
>>>>>> This is a sample given in amber tutorial
>>>>>>
>>>>>> trajin traj.1.gz
>>>>>> trajin traj.2.gz
>>>>>> cluster out testcluster representative pdb average pdb
>>>>>> averagelinkage
>>>>>> clusters 5 rms .CA
>>>>>>
>>>>>> Is the mask part you mentioned "rms .CA" ?
>>>>>>
>>>>>> Are you familiar with mmtsb (i always use mmtsb as learned from
>>>>>> amber
>>>>>> tutorial) ? And do you know any keyword related to this?
>>>>>>
>>>>>> thanking you
>>>>>>
>>>>>> On Thu, Dec 1, 2016 at 3:56 PM, Achim Sandmann <
>>>>>> Achim.Sandmann.chemie.stud.uni-erlangen.de> wrote:
>>>>>>
>>>>>>> Hello Mary Varughese,
>>>>>>>
>>>>>>>
>>>>>>> So far as I understood, you want to take the ligand position with
>>>>>>> respect to the DNA (as well as the ligand conformation itself) into
>>>>>>> consideration.
>>>>>>>
>>>>>>> I think the easiest way to do this is to do a RMSD calculation with
>>>>>>> the
>>>>>>> DNA backbone mask first. This will align the structures. As a
>>>>>>> second
>>>>>>> step (within the same praj/cpptraj call) you can use the cluster
>>>>>>> command
>>>>>>> with the mask of the ligand and the 'nofit' flag.
>>>>>>>
>>>>>>>
>>>>>>> with kind regards,
>>>>>>>
>>>>>>> Achim Sandmann
>>>>>>>
>>>>>>>
>>>>>>>> Am 01.12.2016 um 08:26 schrieb Mary Varughese:
>>>>>>>> Sir
>>>>>>>>
>>>>>>>> I have a DNA ligand system. After aligning all the structures
>>>>>>>> with
>>>>>>> respect
>>>>>>>> to DNA backbone i want to cluster on the basis of ligand
>>>>> conformation. Is
>>>>>>>> there any way to specify that aspect in mmtsb or ptraj cluster.
>>>>>>>>
>>>>>>>> Thanking you
>>>>>>>>
>>>>>>>>
>>>>>>>> mary varughese
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>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> -------------------------
>>>>> Daniel R. Roe
>>>>> Laboratory of Computational Biology
>>>>> National Institutes of Health, NHLBI
>>>>> 5635 Fishers Ln, Rm T900
>>>>> Rockville MD, 20852
>>>>> https://www.lobos.nih.gov/lcb
>>>>>
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>>>>>
>>>>
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Received on Thu Dec 15 2016 - 06:00:02 PST
