Hi all,
I need to load several trajectories with different topologies into cpptraj and then run a single analysis on a common subset of atoms. It seems like this should be possible, but I cannot find the syntax in the Amber14 manual.
I've tried loading each parameter/trajectory pair individually and then running the analysis using the following script:
# Load Coordinates
parm system1.prmtop [data1]
trajin system1.nc 1 last 10 parm [data1]
...
parm system2.prmtop [data2]
trajin system2.nc 1 last 10 parm [data2]
...
parm system3.prmtop [data3]
trajin system3.nc 1 last 10 parm [data3]
...
## Load reference structure
parm reference.prmtop [ref]
reference reference.inpcrd parm [ref]
# Align to reference
rms RMSD :38-58,73-163.CA reference
# Covariance
matrix covar name cvmtrx out cvmtrx.all.dat :13-18,31-37,59-72
analyze matrix cvmtrx out evecs.comp.dat vecs 1206
# Run and finish
run
quit
This runs without complaint, however a different approach to the same problem gives a different outcome. Since the three topologies only differ at one residue (#12, not included in either the RMS fit or the covariance matrix), I removed that residue from the topology and trajectories using the strip command and loaded all of the trajectories with a single parameter file:
# Load Coordinates
parm modified.prmtop [data]
trajin mod.trajectory1.nc 1 last 10 parm [data]
trajin mod.trajectory2.nc 1 last 10 parm [data]
trajin mod.trajectory3.nc 1 last 10 parm [data]
## Load reference structure
parm reference.prmtop [ref]
reference reference.inpcrd parm [ref]
# Align to reference
rms RMSD :38-58,73-163.CA reference
# Covariance
matrix covar name cvmtrx out cvmtrx.all.dat :13-18,31-37,59-72
analyze matrix cvmtrx out evecs.all.dat vecs 1206
# Run and finish
run
quit
For practical reasons, I need to load each trajectory and then combine them in cpptraj. How do I tell cpptraj to apply the mask to all of the data in the first script? I've tried inserting the topology tags into the rms command in every way I can think of, but always get errors. It would also work to have cpptraj strip the differing atoms inline, either by using the 'strip' command or by applying a mask via the 'parm' or 'trajin' commands, if those are feasible.
Thanks,
Gard
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Received on Mon Dec 15 2014 - 18:00:04 PST
