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
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?
if without the option -enzdes:cstfile, remodel can terminates normally, the design result is also reasonable.
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.
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.