Dear Amber users,
Fortunately it works know. You are right Amber program renumber residues
sequentially.
Thanks specially to Dan, Jason, Asaminew for your comments and suggestions,
Best regards
2014-04-24 13:23 GMT+02:00 Jason Swails <jason.swails.gmail.com>:
> On Thu, 2014-04-24 at 10:57 +0200, Marlet Martinez wrote:
> > Dear AMBER users,
> >
> > Seems that the "strip" command was useful for the analysis of each of my
> > protein chains since I could mask the atoms I was not focused for my
> > analysis.
> >
> > The thing is when I am trying to analyze RMSD for the two chains (general
> > RMSD) my out put is always for one the chains. My protein has two chains
> > both named as "C" and numbered equally 20-450,
> >
> > What I have done is for example:
> >
> > rms 20-450.CA reference out allprot.dat : but with this
> I
> > always obtain analysis for just one chain
> >
> > So my question is how could I indicate in this script that I need the
> RMSD
> > analysis for both chains (all the protein) at the same time?
>
> Amber programs renumber residues sequentially. So :20-450.CA
> corresponds only to the first chain that is defined (note that any
> insertion codes or missing residues from the original PDB file are
> discarded and the residues are numbered based on which ones are
> _actually_ there).
>
> If each chain is 500 residues and you only want to compute the RMSD for
> residues 20-450 in each chain, your command would have to look like:
>
> rms :20-450,520-950 out allprot.dat
>
> instead.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Thu Apr 24 2014 - 09:00:02 PDT
