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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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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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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Received on Tue Dec 06 2016 - 12:30:03 PST
