Re: [AMBER] residue stripping in ptraj

From: Thomas Cheatham III <>
Date: Tue, 11 Oct 2011 14:11:03 -0600 (Mountain Daylight Time)

> My protein has 225 residues. I want to do clustering of the trajectory,
> using only a few residues that lie as two different chains in the middle of
> the polypeptide. Thus, I tried to strip only specific residues using ptraj
> so as to exclude the residues that i do not require, using the following
> command :
> trajin abc_dry.mdcrd 1 2000 1
> center :1-225
> strip :1-20
> strip :120-130
> image center familiar
> trajout abc-clust_dry.mdcrd

You have to be careful with the stripping since after each strip the
residue numbers are re-ordered. Also, you will need a PDB or prmtop that
corresponds to the new trajectory in order to process it correctly.

ptraj does not have the ability to magically map atoms to coordinates
since the coordinate file is simple N atoms of X, Y, Z numbers. The
correspondence of atom# to X,Y,Z is determined by the loaded up prmtop (or
PDB file). The observation of fewer frames means that you are loading a
prmtop/PDB that has more atoms than expected per frame.

Let's look at your choices...

> trajin abc_dry.mdcrd 1 2000 1
> center :1-225
> strip :1-20

This strips the first 20 residues, which will not be renumbered so that
residue 21 is 1, 22 is 2, ...

> strip :120-130

This is now effectively stripping what was previously residues :141-151.

I think what you want is:

center :1-225
strip :120-125
strip :1-20
image center familiar
trajout abc-clust_dry.mdcrd
average avg-tmp.pdb pdb start 1 stop 2

(I added the average to dump a PDB file which will show you what the "new"
pdb would look like after stripped).

...or alteratively the strip can be grouped into a single strip command...

center :1-225
image center familiar
strip :1-20,120-130
trajout abc-clust_dry.mdcrd

Of course, if the protein was in two separate molecules, and if the
molecules became unwrapped, you would have to put them together somehow
prior... See the e-mail reflector archive on imaging/wrapping issues.


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Received on Tue Oct 11 2011 - 13:30:02 PDT
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