Dear Xplor mailing list,
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). Can anyone suggest how to proceed? Regards, _________________________________________________________________ Dr. Douglas R. Houston Senior Lecturer in Computational Biochemistry Institute of Quantitative Biology, Biochemistry and Biotechnology Room 3.23, Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20161130/b09105c8/attachment-0001.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: errordir.zip Type: application/x-zip-compressed Size: 36900 bytes Desc: errordir.zip URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20161130/b09105c8/attachment-0001.bin> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20161130/b09105c8/attachment-0001.ksh>
