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tubiana / TTClust

clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)
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Clustering of host guest systems #39

Closed sameersaurav closed 7 months ago

sameersaurav commented 7 months ago

Hi there,

I want to align my trajectory along atoms from, serial 1 to 148. I tried following commands - ttclust -f 200ns.xtc -t Umb_1.pdb -sa "index 1 to 148" tclust -f 200ns.xtc -t Umb_1.pdb -sa "index <= 147"

Error-

NOTE : Extraction of subtrajectory for time optimisation ERROR : there is an error with your selection string SELECTION STRING : backbone

Kindly suggest the correct syntax for sa. Thank you for your help.

tubiana commented 7 months ago

Hi!

-sa is for the alignement of the trajectory. To give a selection for the clustering, the right argument is -sr. If you wanna align and cluster on the selection you gave I suggest to try this command :

ttclust -f 200ns.xtc -t Umb_1.pdb -sa "index 1 to 148" -sr "index 1 to 148"
tclust -f 200ns.xtc -t Umb_1.pdb -sa "index <= 147 -sr "index 1 to 148"

Kind regards Thibault

sameersaurav commented 7 months ago

Dear Thibault,

Thanks a lot.

With regards Sameer