Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › Error when running Remodel with EnzDes constraint file to extend c-terminal
- This topic has 10 replies, 3 voices, and was last updated 7 years, 2 months ago by
Anonymous.
-
AuthorPosts
-
-
January 19, 2017 at 2:20 pm #2570
Anonymous
hi, everybody
In my test in running Remodel with EnzDes constraint file,
the blueprint file is:
””
95 E .
96 F . CST1A
97 S .
98 E L CST1B
99 E L
#################
the cstfile is:
CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_type: Nbb
TEMPLATE:: ATOM_MAP: 1 is_backbone
TEMPLATE:: ATOM_MAP: 1 residue3: ALA CYS ASP GLU PHE GLY HIS ILE LYS LEU MET ASN GLN ARG SER THR VAL TRP TYR
TEMPLATE:: ATOM_MAP: 2 atom_type: Nbb
TEMPLATE:: ATOM_MAP: 2 is_backbone
TEMPLATE:: ATOM_MAP: 2 residue3: ALA CYS ASP GLU PHE GLY HIS ILE LYS LEU MET ASN GLN ARG SER THR VAL TRP TYR
CONSTRAINT:: distanceAB: 6.62 0.2 1.00 0
CST::END
#################
the flag for remodel command is:
……./remodel.default.linuxgccrelease -database … … -s 2LV8.pdb -run:chain A -remodel:num_trajectory 2 -remodel:quick_and_dirty -overwrite -enzdes:cstfile cstfile
##################
Remodel exits with the following error:
terminate called after throwing an instance of ‘boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::bad_weak_ptr> >’
what(): tr1::bad_weak_ptr
Got some signal… It is:6
Process was aborted!
protocols.toolbox.match_enzdes_util.EnzConstraintIO: read enzyme constraints from cstfile …
protocols.toolbox.match_enzdes_util.EnzConstraintIO: WARNING: Message(s) above was printed in the end instead of proper place because this Tracer object has some contents left in inner buffer when destructor was called. Explicit call Tracer::flush() or end your IO with std::endl to disable this warning.
#################
I have already read the web pages
https://www.rosettacommons.org/node/3263
https://www.rosettacommons.org/docs/latest/application_documentation/design/rosettaremodel
but I can’t find format error in my input file. it confused me
-
January 21, 2017 at 5:58 pm #12107
What happens if you run Remodel without the constraints? Do you get any error messages and does your output structure looks like you’d expect?
-
January 21, 2017 at 5:58 pm #12628
What happens if you run Remodel without the constraints? Do you get any error messages and does your output structure looks like you’d expect?
-
January 21, 2017 at 5:58 pm #13149
What happens if you run Remodel without the constraints? Do you get any error messages and does your output structure looks like you’d expect?
-
January 22, 2017 at 2:14 am #12108
if without the option -enzdes:cstfile, remodel can terminates normally, the design result is also reasonable.
-
January 22, 2017 at 2:14 am #12629
if without the option -enzdes:cstfile, remodel can terminates normally, the design result is also reasonable.
-
January 22, 2017 at 2:14 am #13150
if without the option -enzdes:cstfile, remodel can terminates normally, the design result is also reasonable.
-
January 23, 2017 at 7:04 pm #12114
In your pasted CST above, the line CONSTRAINT is the same level of indentation as CST::END. Is that also true in your file?
You could also try replacing residue3 with residue1 and the corresponding one letter amino acids (residue1: AGSITN….) and see if that has any effect.
-
January 23, 2017 at 7:04 pm #12635
In your pasted CST above, the line CONSTRAINT is the same level of indentation as CST::END. Is that also true in your file?
You could also try replacing residue3 with residue1 and the corresponding one letter amino acids (residue1: AGSITN….) and see if that has any effect.
-
January 23, 2017 at 7:04 pm #13156
In your pasted CST above, the line CONSTRAINT is the same level of indentation as CST::END. Is that also true in your file?
You could also try replacing residue3 with residue1 and the corresponding one letter amino acids (residue1: AGSITN….) and see if that has any effect.
-
October 17, 2017 at 6:52 pm #13820
Hi guys. I’m facing the same problem here.
Below are the error messages using my personal Mac:
#####
libc++abi.dylib: terminating with uncaught exception of type std::__1::bad_weak_ptr: bad_weak_ptr
Got some signal… It is:6
Process was aborted!
protocols.toolbox.match_enzdes_util.EnzConstraintIO: read enzyme constraints from cst.file2 …
protocols.toolbox.match_enzdes_util.EnzConstraintIO: WARNING: Message(s) above was printed in the end instead of proper place because this Tracer object has some contents left in inner buffer when destructor was called. Explicit call Tracer::flush() or end your IO with std::endl to disable this warning.
####
Trying to run the same protocol using my lab’s cluster, I’ve got the similar problem:
####
terminate called after throwing an instance of ‘boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::bad_weak_ptr> >’
what(): tr1::bad_weak_ptr
Got some signal… It is:6
Process was aborted!
protocols.toolbox.match_enzdes_util.EnzConstraintIO: (0) read enzyme constraints from cst.file2 …
protocols.toolbox.match_enzdes_util.EnzConstraintIO: (0) WARNING: Message(s) above was printed in the end instead of proper place because this Tracer object has some contents left in inner buffer when destructor was called. Explicit call Tracer::flush() or end your IO with std::endl to disable this warning.
####
Follow below my cst.file2:
CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_type: Nbb
TEMPLATE:: ATOM_MAP: 1 is_backbone
TEMPLATE:: ATOM_MAP: 1 residue1: ADEFGHIKLMNQRSTVWY
TEMPLATE:: ATOM_MAP: 2 atom_type: OCbb
TEMPLATE:: ATOM_MAP: 2 is_backbone
TEMPLATE:: ATOM_MAP: 2 residue1: ADEFGHIKLMNQRSTVWY
CONSTRAINT:: distanceAB: 3.00 0.20 100.00 1
CST::END
I also have tried using residue3 (3 letters aminoacid codes), but got same error.
Any help is more than welcome!
Thanks in advance.
-
-
AuthorPosts
- You must be logged in to reply to this topic.