Hello Jonesy--
>
> I am trying to generate initial .pdb structures for a peptide RNA complex.
> ?My peptide contains nonstandard amino acids; I have already added their
> topology data to protein.top. ?When I try to run my script in xplor, I keep
> getting the following errors (see attached). ?I have checked to see that my
> NOE table assignments match what I have put into the topology file, but I am
> not sure what else to check from here.
>
> X-PLOR>structure @cmplx3.tmplt.pdb end
> ASSFIL: file cmplx3.tmplt.pdb opened.
> STRUcture>REMARK FILENAME="cmplx3.tmplt.pdb"
> STRUcture>REMARK produced by nmr/generate_template.inp
> STRUcture>REMARK DATE:02-May-13 13:17:19 created by user: jonesy
> STRUcture>ATOM 1 N DAB 1 13.356 -4.230 -4.022 1.00 0.00
> JB18
> %STRUcture-ERR: unrecognized command:
> ATOM
It looks like you specified a pdb file where a psf file should be. You
might want to try the Python interface instead of the old XPLOR
interface. However, you will still need a psf file because you are
using nonstandard residues. Please let me know if you have further
issues.
best regards--
Charles
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--
Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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