Hello Douglas-- > > I am encountering a confusing error when trying to refine the NMR > structure of a stapled peptide. I initially thought the problem was > caused by the staple part, but on closer inspection of the error > messages, it appears to be failing to find sensible covalent > geometry for two leucines that are present in the peptide (see > xplor_in.log in attached zip of run directory). Raising > maxFixupIters to 10000 has not helped. > > Before Xplor, I performed energy minimisation in NAMD using the .psf > so I assume it and the output .pdb are OK (in VMD they certainly > look OK to my eye, including the leucines). >
The default Xplor-NIH tolerances are quite tight - to detect parameter inconsistencies, and it seems that parameters you're using don't quite meet this standard - the CG leucine angles can't be satisfied within the default tolerance of 2 degrees. The easiest thing to do is to relax the tolerance slightly- relaxing the tolerance to 3.5 degrees seems to do the trick. Please see the attached script. best regards-- Charles
xplor_in.py
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