Dear all,
I've been doing some clustering analysis on an RNA trajectory using ptraj (AmberTools 13). Because the trajectory is quite long, I need to use the sieving option, at least for some of the clustering algorithms.
I've been running different algorithms and trying different cluster counts to compare the results by looking at the DBI and pSF statistics. However this values do not come out in the cluster.txt file because I'm using the sieve option. In the EndFistPass file, The SSR/SST value is <0.6 in all cases. I guess it is so low because only a subset of frames are included in this pass, so I'm hoping that for the whole trajectory SSR/SST would be closer to 1.
I read in the AmberTools Manual that "The DBI and pSF values (SSR/SST too?) for a sieving algorithm can be calculated later by running the ptraj clustering again, using “DBI” as the algorithm. This will read the clustering result from the “filename.txt” and appended the DBI and pSF values to the file "filename.txt”".
Sorry for being so thick, but could someone please give me an example of syntax for this? Following the manual, I've tried to write DBI instead of the name of the clustering algorithm, but it won't go past the first pass.
So, for example, here:
prnlev 5
trajin ../../../40C_1N8R1-15.1.dry.trj
cluster out cluster40C.1_1N8R_means representative pdb \
average pdb means sieve 100 clusters 15 rms mass :2-20
but it's obviously not as simple as doing this (because this doesn't work):
prnlev 5
trajin ../../../40C_1N8R1-15.1.dry.trj
cluster out cluster40C.1_1N8R_means representative pdb \
average pdb DBI sieve 100 clusters 15 rms mass :2-20
I've tried removing other parts of the script, but I'm afraid I need some help to understand this a bit better. I couldn't find any related information on previous amberlist posts.
Thank you very much in advance.
Amparo
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Received on Fri Jun 21 2013 - 07:00:02 PDT
