Hi, I get this message at the start of my structure calculations:
round10_new.py(278): randomizeTorsions(dyn) AT_Build::buildNode: cycle link found between atoms 28 PRO 3 CD and 19 PRO 3 N removing bond. AT_Build::buildNode: cycle link found between atoms 74 PHE 7 CD2 and 71 PHE 7 CG removing bond. AT_Build::buildNode: cycle link found between atoms 948 PHE 69 CD2 and 945 PHE 69 CG removing bond. AT_Build::buildNode: cycle link found between atoms 1090 PRO 78 CD and 1081 PRO 78 N removing bond. AT_Build::buildNode: cycle link found between atoms 1180 TYR 86 CD2 and 1177 TYR 86 CG removing bond. AT_Build::buildNode: cycle link found between atoms 1238 PHE 90 CD2 and 1235 PHE 90 CG removing bond. AT_Build::buildNode: cycle link found between atoms 1309 PHE 95 CD2 and 1306 PHE 95 CG removing bond. AT_Build::buildNode: cycle link found between atoms 1993 PHE 146 CD2 and 1990 PHE 146 CG removing bond. AT_Build::buildNode: cycle link found between atoms 2122 TYR 156 CD2 and 2119 TYR 156 CG removing bond. AT_Build::buildNode: cycle link found between atoms 2273 TYR 169 CD2 and 2270 TYR 169 CG removing bond. AT_Build::buildNode: cycle link found between atoms 2314 PRO 172 CD and 2305 PRO 172 N removing bond. AT_Build::buildNode: cycle link found between atoms 2346 PRO 175 CD and 2337 PRO 175 N removing bond. AT_Build::buildNode: cycle link found between atoms 2392 PRO 179 CD and 2383 PRO 179 N removing bond. AT_Build::buildNode: cycle link found between atoms 2425 TYR 182 CD2 and 2422 TYR 182 CG removing bond. AT_Build::buildNode: cycle link found between atoms 2445 PRO 183 CD and 2436 PRO 183 N removing bond. AT_Build::buildNode: cycle link found between atoms 2466 PRO 185 CD and 2457 PRO 185 N removing bond. AT_Build::buildNode: cycle link found between atoms 2530 PRO 191 CD and 2521 PRO 191 N removing bond. AT_Build::buildNode: cycle link found between atoms 2545 PHE 192 CD2 and 2542 PHE 192 CG removing bond. AT_Build::buildNode: cycle link found between atoms 2607 PHE 197 CD2 and 2604 PHE 197 CG removing bond. round10_new.py(282): from varTensorTools import calcTensorOrientation round10_new.py(288): InitialParams( rampedParams ) I've read in the mailing list that this pops up with disulfide bonds or metal ion binding. How do I prevent XPLOR from removing those bonds, which should be there. Is there a setting somewhere? Thanks -- Marie-Laurence Tremblay, PhD candidate Department of Biochemistry and Molecular Biology Dalhousie University 5850 College St. Halifax NS, Canada B3H 1X5 mltremblay at dal.ca Phone:902-494-4812 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20130319/c880dd01/attachment.html
