?Hello, ?I'm having trouble using an XPLOR script that you originally gave to Jordan Burke to refine the structure of an RNA using data from SAXS, RDCs, and minimal additional NMR data. Have you ever encountered this error before?
?This is the end of the log file: ?X-PLOR> ?X-PLOR>end ?[stdin](428): protocol.initDynamics(dyn, ?[stdin](429): initVelocities=1, ?[stdin](430): bathTemp=init_t, ?[stdin](431): potList=potList, ?[stdin](432): numSteps=10000, ?[stdin](433): finalTime=10) ?[stdin](434): dyn.run() ?HBONDS: allocating space for 2025 h-bond interactions. ?HBONDS: 0 distance exclusions and 0 angle exclusions ?HBONDS: 205918 fixed h-bonds, currently 0 h-bonds present ?HBONDS: allocating space for 2025 h-bond interactions. ?HBONDS: ran out of space. Starting over. ?HBONDS: allocating space for 4050 h-bond interactions. ?HBONDS: 200042 distance exclusions and 3334 angle exclusions ?HBONDS: 0 fixed h-bonds, currently 2542 h-bonds present ?MAKINB: mode 3 found 0 exclusions, 0 interactions(1-4) and 0 GB exclusions ?MAKINB: mode 3 found 8922 exclusions, 0 interactions(1-4) and 8922 GB exclusions ?HEAP: maximum use=440784760 current use=436363876 ?X-PLOR: total CPU time= 3398.3701 s ?X-PLOR: entry time at 17:05:14 28-Mar-13 ?X-PLOR: exit time at 18:06:20 28-Mar-13 I've attached my script. When I comment out the dynamics step before the anneal, the last part of the log file is: AT_Build::buildNode: cycle link found between atoms 2808 GUA 88 C3' and 2784 GUA 88 C4' removing bond. AT_Build::buildNode: cycle link found between atoms 2834 GUA 89 C5 and 2824 GUA 89 C4 removing bond. AT_Build::buildNode: cycle link found between atoms 2836 GUA 89 C8 and 2823 GUA 89 N9 removing bond. AT_Build::buildNode: cycle link found between atoms 2842 GUA 89 C3' and 2818 GUA 89 C4' removing bond. AT_Build::buildNode: cycle link found between atoms 2858 CYT 90 C6 and 2857 CYT 90 N1 removing bond. AT_Build::buildNode: cycle link found between atoms 2873 CYT 90 C3' and 2852 CYT 90 C4' removing bond. HBONDS: allocating space for 2025 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 205918 fixed h-bonds, currently 0 h-bonds present HBONDS: allocating space for 2025 h-bond interactions. HBONDS: ran out of space. Starting over. HBONDS: allocating space for 4050 h-bond interactions. HBONDS: 200042 distance exclusions and 3334 angle exclusions HBONDS: 0 fixed h-bonds, currently 2542 h-bonds present MAKINB: mode 3 found 0 exclusions, 0 interactions(1-4) and 0 GB exclusions MAKINB: mode 3 found 8922 exclusions, 0 interactions(1-4) and 8922 GB exclusions HEAP: maximum use=440784760 current use=436363876 X-PLOR: total CPU time= 3326.4299 s X-PLOR: entry time at 19:25:21 31-Mar-13 X-PLOR: exit time at 20:25:07 31-Mar-13 If you have any suggestions on how to fix this, that would be great! Thank you! Allison Didychuk Butcher Lab -------------- next part -------------- A non-text attachment was scrubbed... Name: U4U6-xplor-no-rigid_DC1.py Type: application/octet-stream Size: 13710 bytes Desc: not available Url : http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20130401/e33d5411/attachment-0001.obj
