Hello,
I have a project in Anaylsis with a non-standard which I am exporting to ARIA 2.3. Everything seems to go ok, the psf and pdb files are created, however the following error is generated before the structure calculation:
ValueError: USER ERROR <aria.ConversionTable.ConversionTable> File "/home/chxcw/Programs/aria2.3/src/py/aria/ConversionTable.py", line 193 in convert_atom
Residue "" of type "AMINO_ACID" not known.
I can generate structures using ARIA xml files, the psf and pdb files are generated correctly and the calculation proceeds normally. The error seems to be coming from the files generated by Analysis. The sequence is extracted by Analysis and converted to a pdb file in the run dir generated by ARIA (cns/data/sequence) , however for the non-standard residues there is a gap (see below). This file seems to get rewritten each time aria is run, so replacing it with a correctly labelled pdb file doesn't help. I have other molecules in the same project with other non-standard residues and these work fine. Is there any way to export this file with the correct residue name? The ChemComp and ChemCompCoord xml files from Chembuild have a ccp and 3Letter code in the header and it shows up in the atom browser.
ATOM 286 HD2 LYS 19 0.000 0.000 0.000 0.00 0.00 A
ATOM 287 HN LYS 19 0.000 0.000 0.000 0.00 0.00 A
ATOM 288 HB1 LYS 19 0.000 0.000 0.000 0.00 0.00 A
ATOM 289 HB2 LYS 19 0.000 0.000 0.000 0.00 0.00 A
ATOM 290 O' 20 0.000 0.000 0.000 0.00 0.00 A
ATOM 291 CD1 20 0.000 0.000 0.000 0.00 0.00 A
ATOM 292 CD2 20 0.000 0.000 0.000 0.00 0.00 A
ATOM 293 HA 20 0.000 0.000 0.000 0.00 0.00 A
ATOM 294 HE1 20 0.000 0.000 0.000 0.00 0.00 A
ATOM 295 HE2 20 0.000 0.000 0.000 0.00 0.00 A
Chris
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