Re: [AMBER] ired analysis: No modes data specified

From: David A Case <>
Date: Tue, 4 Aug 2015 09:44:13 -0400

On Tue, Aug 04, 2015, Kris Feher wrote:

> rms first out wAnTx_prodNPT-100ns.rmsfit .CA, C,N time 0.01
> center :1-20
> image familiar
> strip :WAT
> strip :Cl-

You should have received lots of error messages/warnings from your first
cpptraj run.

First: you cannot have spaces in the atom selection. Use this:

The "time" option doesn't make any sense for an rms operation.

After you do an RMS fit, you can no longer image the trajectory. If you have
only a single chain as a macromolecule, there is probably no need to image
the trajectory at all: just strip the waters and ions first, then use that
trajectory for subsequent ired analysis.

I'm not sure if these problems are leading to the further problems you find in
the second cpptraj step, but they should certainly be addressed.

> vector v2 :2 ired :2

This is not correct: you are constructing a vector from to center of mass
of residue 2 *to* the center of mass of residue 2: i.e. a null vector.

See Section 29.14.5 for examples of ired analysis. You generally want to
define (for example) N-H vectors in various residues.

...hope this helps....dac

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Received on Tue Aug 04 2015 - 07:00:02 PDT
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