On Thu, Feb 09, 2012, Olena Dobrovolska wrote:
>
> I have another protein, and the first 25 amino acids are unstructured,
> so I ran CYANA only for structured region (starting from 26th amino
> acid). When I want to perform a minimization, on the stage of creating
> prmtop and crd file I save the updated pdb file. But the problems is
> that in pdb file the residue number starts from 1, but it should be from
> 26th. Thus I can't generate RST.dist file since dist and pdb files are
> not compatible anymore. Is there a way to make it start count from 26nd
> amino acid in pdb file?
This is indeed a pain. You pretty much have to edit the 7col (or 8col) file
input to makeDIST_RST to use the same residue numbers as in the pdb file you
got from LEaP. An awk or perl script can often be very useful in doing things
like this.
....dac
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Received on Thu Feb 09 2012 - 09:00:04 PST
