Re: [AMBER] Using the rep.C0.pdb as a reference structure in RMSD analysis

From: Daniel Roe <>
Date: Wed, 25 Nov 2020 10:18:33 -0500


On Tue, Nov 24, 2020 at 10:56 AM Soheila Shokrollahzade
<> wrote:
> parm
> trajin
> reference rep.c0.pdb [c0]
> rms RMSD ref [c0]

This should work. Check the output to make sure. Be aware though this
will use all atoms since there is no atom mask provided. Again, the
output of the command will let you know what it's doing.

> rms RMSD .CA,C,N,O out c0.txt
> rms FIT .CA,C,N,O to-reference.txt

Since you didn't specify a reference structure for either of these
commands, it will use the default (first frame). The output should say
that this is what is happening. If you want to use rep.c0.pdb you need
to specify that with 'reference', 'ref [c0]', etc.

> quit

You're quitting before you run - either put a 'run' before 'quit', or
just omit 'quit' (if running in batch mode, i.e. with an input

Hope this helps,


> Thank you,
> Soheila
> --
> *PhD student of Biomedical Engineering, Garton lab
> <>*
> *Institute of Biomedical Engineering (BME) *
> *University of Toronto*
> *Room 422, Rosebrugh building, 164 College Street, Toronto, ON, M5S 3E2*
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Received on Wed Nov 25 2020 - 07:30:04 PST
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