Hi,
I have the following setup: 20 models each having N short independent
simulations. Models differ in the amino acid composition (all atom
topologies are different) however their length is the same (backbone
topologies match each other).
I would like to perform combined clustering on the backbone atoms of all
trajectories for all models and obtain all atom representative structures.
Above approach works if I have only one model when I use the following
CPPTRAJ input:
parm A.parm7
trajin 1.nc
trajin 2.nc
(... this goes N times...)
rms first .C,CA,O,N out A.rmsd
cluster out ... summary ... info .... repout .... repfmt pdb averagelinkage
clusters ... rms nofit .C,CA,O,N
However I wonder if it's possible to use cpptraj to perform similar
analysis on e.g. 20 models. Here's what I worked out so far:
parm A.parm7 [A]
trajin A1.nc parm [A]
trajin A2.nc parm [A]
(... this goes N times...)
parm B.parm7 [B]
trajin B1.nc parm [B]
trajin B2.nc parm [B]
(... this goes N times ...)
(... this goes for each model)
rms first .C,CA,O,N out A.rmsd
cluster out ... summary ... info .... repout .... repfmt pdb averagelinkage
clusters ... rms nofit .C,CA,O,N
Which results in the: Error: # atoms in current topology (1429) != # atoms
in coords set "_DEFAULTCRD_" (1449) (printed for each model with diffreent
atom number).
I tried also with stripping the trajectories with mask "!(.C,CA,O,N)"
however I suspect that with this approach I won't be able to retain full
atom representative structures.
Concluding, I would like to ask whether it is possible to perform this kind
of analysis in CPPTRAJ in a single run.
Many thanks in advance,
Jan Ludwiczak
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 13 2017 - 05:00:03 PST
