Hello Allison--
>
> ?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 don't see any errors here.
>
> 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.
These warnings are due to not calling torsionTopology or cartesianTopology
> 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
Again, no errors- these are informational messages.
What sort of problems are you having?
Charles
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--
Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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