Dear Amber users,
I have been trying to understand the flexibility of transcription mediator protein and I have an NMR ensemble structure downloaded from RCSB. There are 10 conformers in the .pdb file and I have run normal MD simulations (NPT) 100 ns each for each model.
Now I want to perform clustering of each of my 10 runs (run 1 is model1.pdb, run2 is model2.pdb, so on.. till run 10..model10.pdb) , so that I can get an idea of whether the structures are all converging to an approximate structure or not, and finally calculate RMSDs between the most populated clusters
**I have not done extensive clustering in AMBER18** so please forgive me if there are errors in my input file
This is my input file:
All I need to know is what are the results I am expecting once I do a cpptraj command line on my input file. I do not want to run it as a black box. ( I have opted DBSCAN just randomly, please suggest if its not appropriate and any specific algorithms I may be needing to use)
Thank you all.
parm 2XXX_solvated.prmtop
trajin 2XXX_prod1.mdcrd 1 100000 10
###we are worried about protein conformations, and hence we don’t need to bother about solvents and ions during the clustering procedure!
strip :Cl-,Na+,WAT
center mass origin :1-152
image origin center
#Align trajectory to reference structure by minimizing RMSD
reference 2XXX_imaged_run1.pdb
rms reference mass out RMSD_CA.txt :2-151.CA,C,N
cluster cluster_out dbscan minpoints 20 epsilon 1 rms :2-151.CA,C,N out combined.dat summary summary.out info data_run1_water_cluster singlerepout clusters.pdb singlerepfmt pdb
go
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Received on Mon Feb 24 2020 - 09:30:02 PST
