Re: [AMBER] Analyzing multiple trajectories in cpptraj

From: Gard Nelson <Gard.Nelson.NantBio.com>
Date: Tue, 16 Dec 2014 17:50:11 +0000

Thanks for your suggestion, Dan. That fixed it.

Gard

-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Monday, December 15, 2014 7:21 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Analyzing multiple trajectories in cpptraj

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
(801) 585-6208 (Fax)
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Received on Tue Dec 16 2014 - 10:00:02 PST
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