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

Date: Wed, 23 Jan 2019 19:18:35 +0000

ah great! the chain* was definitely something I wouldn’t have figured out as well as the writedata details.

Thank you Dac! This is much appreciated!

> On Jan 23, 2019, at 11:32 AM, David A Case <> wrote:
> 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
> run
> writedata vectraj trajfmt netcdf parmout comvectors.parm7 noorigin chain*
> go
> 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.
> ....dac
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Received on Wed Jan 23 2019 - 11:30:01 PST
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