Dea Xplor mailing list,
I'm trying to refine an NMR structure of a "stapled" peptide, but keep getting an error regarding a "cycle link" and a segmentation fault: AT_Build::buildNode: cycle link found between atoms 90 OL8 7 CB and 86 OL8 7 CA removing bond. MAKINB: mode 3 found 600 exclusions, 0 interactions(1-4) and 600 GB exclusions MAKINB: mode 3 found 0 exclusions, 0 interactions(1-4) and 0 GB exclusions *--- Dynamics ---- step= 0 ---- time= 0 ---- delta_t= 0.001 --* | E(kin)+E(poten)= 1095.571 E(kin)= 298.981 temperature= 3458.710 | | E(poten)= 796.5907439 grad= 51.8135409 ANGL= 29.1910614 | | BOND= 0.3841119 CDIH= 618.9753810 HBDB= 0.0000000 | | IMPR= 0.0000000 VDW= 70.4441474 Vgyr= 0.0001693 | | jcoup= 16.5281005 noe= 60.6248660 torsionDB= 0.4429064 | *------------------------------------------------------------------------------* /opt/xplor-nih-2.41.1/bin/xplor: line 548: 30082 Segmentation fault /opt/xplor-nih-2.41.1/bin.Linux_x86_64/xplor '-py' 'xplor_in.py' It's not completely reproducible, sometime it will generate 1 or 2 of the 20 structures requested in the script, but it never makes it to the end. No doubt it's caused by the olefin "staple" (note the modified lipid paramaters file, I took the parameters for a couple of atom types (for the alkene) from my NAMD CHARMM22 parameter file) but more than that I can't tell. I attach all the relevant files. Any help would be appreciated. _________________________________________________________________ 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/20161017/89585321/attachment-0001.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: parallh22x.pro Type: application/octet-stream Size: 138776 bytes Desc: parallh22x.pro URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20161017/89585321/attachment-0002.obj> -------------- next part -------------- A non-text attachment was scrubbed... Name: aS_min_renum_psfgen.pdb Type: application/x-aportisdoc Size: 16798 bytes Desc: aS_min_renum_psfgen.pdb URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20161017/89585321/attachment-0002.bin> -------------- next part -------------- A non-text attachment was scrubbed... Name: xplor_in.py Type: text/x-python Size: 9056 bytes Desc: xplor_in.py URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20161017/89585321/attachment-0001.py> -------------- next part -------------- A non-text attachment was scrubbed... Name: aS_min_renum_psfgen.psf Type: application/x-font-linux-psf Size: 49876 bytes Desc: aS_min_renum_psfgen.psf URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20161017/89585321/attachment-0003.bin> -------------- next part -------------- A non-text attachment was scrubbed... Name: parallh22x_ole.lip Type: application/octet-stream Size: 27443 bytes Desc: parallh22x_ole.lip URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20161017/89585321/attachment-0003.obj> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20161017/89585321/attachment-0001.ksh>
