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Floppytail modelling

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Floppytail modelling


sorry if this question is too basic, but I'm trying to use FloppyTail to model the C-terminus of a structure (the starting model was generated with robetta) and the run allways crashed.

when I run the test available (complex_readytail_final_nozn.pdb) the program works fine!

I tried many things with the pdb file, but I allways have the same problem

the options are basically the same as the test, obviusly changing the -flexible_start_resnum

the log:

Warning: no movable positions in ShearMover!
apps.public.scenarios.FloppyTail: 96 -169.666 -169.666
Warning: no movable positions in SmallMover!
apps.public.scenarios.FloppyTail: 97 -169.666 -169.666
Warning: no movable positions in SmallMover!
apps.public.scenarios.FloppyTail: 98 -169.666 -169.666
Warning: no movable positions in SmallMover!
apps.public.scenarios.FloppyTail: 99 -169.666 -169.666
apps.public.scenarios.FloppyTail: 100 -169.666 -169.666
apps.public.scenarios.FloppyTail: centroid score of final perturbed PDB: -169.666
apps.public.scenarios.FloppyTail: ------------------------------------------------------------
Scores Weight Raw Score Wghtd.Score
vdw 1.000 0.967 0.967
cenpack 1.000 -5.664 -5.664
hbond_sr_bb 1.000 -92.384 -92.384
hbond_lr_bb 1.000 -45.734 -45.734
pair 1.000 -8.604 -8.604
rama 1.000 -42.406 -42.406
env 1.000 -52.043 -52.043
cbeta 1.000 76.202 76.202
Total weighted score: -169.666
apps.public.scenarios.FloppyTail: One perturb took 0.5 seconds
apps.public.scenarios.FloppyTail: perturb steps complete
core.pack.task: Packer task: initialize from command line()
Segmentation fault

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Fri, 2011-06-24 09:23

Did you change line 447 of to read "false" instead of "true"? (The documentation explains the problem but still says the line number from 3.1 instead of 3.2; it's been fixed for 3.3). It's not clear that that's your problem, it looks like your segfault occurs earlier, but that's far-and-away the most likely issue.

FloppyTail has proven to be vastly more popular than I expected it to be, so I've been tweaking out some things from its original paper (like the analysis suite that is likely causing your crash) to make it more compatible with other uses. The 3.3 release will fully support N-terminal tails and "internal" tails.

If that's not the problem, then it's probably related to whatever is causing those unexpected "Warning: no movable positions in SmallMover!" warnings. What are your values for the flags controlling the flexible region (start, end, and chain), and what are the PDB residue IDs for those?

Fri, 2011-06-24 09:40


thanks for the response

the problem is now solved

Fri, 2011-06-24 10:42