Hi,
Have you applied the latest update (14.22)? This specifically
addresses an issue with 'matrix covar' and multiple topologies which
may be the cause of the strange behavior.
-Dan
On Mon, Dec 15, 2014 at 6:37 PM, Gard Nelson <Gard.Nelson.nantbio.com> wrote:
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Mon Dec 15 2014 - 19:30:02 PST
