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
-- Charles Schwieters email: [email protected] www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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