Hello Mary Varughese,
the mask part is only the ".CA"
my input files look somewhat like this:
trajin sample.ndf start 1 stop 999999 step 10
rms first out sample_rms_referencefit.txt .O1P,O2P #(this file is
of no further use for me)
rms first out sample_rms.txt 1-20,30-32.CA nofit
cluster averagelinkage clusters 10 1-20,30-32.CA out sample.cls summary
sample.sum repout pdb/ repfmt pdb clusterout sample clusterfmt netcdf nofit
go
I'm not familiar with mmtsb.
with kind regards,
Achim Sandmann
Am 01.12.2016 um 11:43 schrieb Mary Varughese:
> 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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>>
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Received on Thu Dec 01 2016 - 04:00:02 PST
