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 - 04:30:03 PDT
