Error when running Remodel with EnzDes constraint file to extend c-terminal

[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&nbsp;

https://www.rosettacommons.org/docs/latest/application_documentation/design/rosettaremodel

but I can’t find format error in my input file. it confused me

[Anonymous]

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?

[Anonymous]

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?

[Anonymous]

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?

[Anonymous]

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

[Anonymous]

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

[Anonymous]

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

[Anonymous]

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. 

[Anonymous]

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. 

[Anonymous]

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. 

[Anonymous]

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.

[Author]

Posts