On 04/01/13, Allison Didychuk wrote: > Hello, > > I'm having trouble using an XPLOR script 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
U4U6-xplor-no-rigid_DC1.py
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