Re: [AMBER] Creating a coarse-grained trajectory from an all atomistic simulation

From: David A Case <>
Date: Wed, 23 Jan 2019 13:32:44 -0500

On Wed, Jan 23, 2019, SARAH JEANNE LEFAVE wrote:
>Is it possible to essentially create a coarse-grain trajectory, using
>coordinates of either each residues center of mass or the alpha carbon
>position, from an all atomistic trajectory? I have experimented with the
>‘vector’ command in cpptraj, but have only been able to get the center
>of mass coordinate for either 1 residue or the entire protein.

Trick is to use lots of vector commands. Here is the structure of an
input file for cpptraj that creates a trajectory of the centroid of CA
positions for each of 343 chosen molecules:

parm ../4lzt_343uc.parm7
reference ../4lzt_343uc.rst7
trajin ../
trajin ../
vector chain1 center ^1.CA # gives centroid position for molecule 1
vector chain2 center ^8.CA
vector chain3 center ^15.CA
vector chain4 center ^22.CA
vector chain5 center ^29.CA
vector chain6 center ^36.CA
vector chain7 center ^43.CA


vector chain341 center ^2381.CA
vector chain342 center ^2388.CA
vector chain343 center ^2395.CA
writedata vectraj trajfmt netcdf parmout comvectors.parm7 noorigin chain*

Key is in the (to me) non-obvious arguments to the writedata command:
script is writing vectors to an output netcdf file ( , but
stripping the origins of those vectors ("noorigin"), so you just get
the positions themselves. The script is also preparing a prmtop file
(comvectors.parm7) that can be used when reading this back into cpptraj
for further manipulations.

Note also the "run" command in the middle: one needs to construct all
the vectors, then essentially start over with the writedata command.
Also the "chain*" construct will expand to all the chains defined above,
in this case from chain1 to chain343.

....hope this helps...don't be afraid to experiment. One needs to learn
to "think like Dan does", (or ask him for help) to do some of this.


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Received on Wed Jan 23 2019 - 11:00:02 PST
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