Re: [rDock-list-def] [rdock-list-def] Segmentation fault when trying to start rdock

[Sergio R. C. <sru...@gm...>]

Hi Ivan,

Thanks for your interest on rDock.
Did you run it from the sourceforge code, github or the pre-compiled
version? If you managed to compile it but you get the segmentation error,
it is hard to know the reason without more information.
I would recommend to try and install one of the dev branches from github,
since there have been some improvements recently:

https://github.com/CBDD/rDock/tree/dev-2021

Thanks again,
Sergio

On Wed, 4 May 2022 at 22:48, Ivan Poplavskiy <pop...@en...>
wrote:

> Hello Everyone,
>
> I tried to run rdock with the default settings described in the
> documentation with the 1koc test, but got a Segmentation fault, what could
> be the problem?
> Starting program: /home/didges/entroforce/rDock/bin/rbdock -i
> actives_final.sdf -o rdock_out -r sys_def.prm -p dock.prm
> ***********************************************
> The rDock program is licensed under GNU-LGPLv3.0.
> http://rdock.sourceforge.net/
> Executable: rbdock ($Id:
> //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $)
> Library: libRbt.so/2013.1/901 2013/11/27
> RBT_ROOT: /home/didges/entroforce/rDock/
> RBT_HOME: /home/didges
> Current dir:    /home/didges/entroforce/rdock_tests/ada
> Date:        Wed May 4 15:03:31 2022
> ***********************************************
>
> Command line args:
>  -i actives_final.sdf
>  -r sys_def.prm
>  -p dock.prm
>  -o rdock_out
>  -n 1 (default)
> Reading polar hydrogens only from ligand SD file
>
> DOCKING PROTOCOL:
> dock.prm
>
> RECEPTOR:
> sys_def.prm
> 4dfr oxido-reductase
>
> DOCKING SITE
> Total volume 509.5 A^3
> Cavity #1 Size=4076 points; Vol=509.5 A^3; Min=(-3,-2,26);
> Max=(9,12,36.5); Center=(4.01607,5.29232,31.2635); Extent=(12,14,10.5)
>
> Program received signal SIGSEGV, Segmentation fault.
>
> gdb gave this result:
>
> 0x00007ffff7e26705 in __gnu_cxx::__normal_iterator<SmartPtr<RbtBond>*,
> std::vector<SmartPtr<RbtBond>, std::allocator<SmartPtr<RbtBond> > >
> std::__find_if<__gnu_cxx: :__normal_iterator<SmartPtr<RbtBond>>*,
> std::vector<SmartPtr<RbtBond>, std::allocator<SmartPtr<RbtBond> > >,
> __gnu_cxx::__ops::_Iter_pred<Rbt::isBond_eq> >(__gnu_cxx:
> :__normal_iterator<SmartPtr<RbtBond>>*, std::vector<SmartPtr<RbtBond>,
> std::allocator<SmartPtr<RbtBond> > >,
> __gnu_cxx::__normal_iterator<SmartPtr<RbtBond>*, std:
> :vector<SmartPtr<RbtBond>, std::allocator<SmartPtr<RbtBond> > >,
> __gnu_cxx::__ops::_Iter_pred<Rbt::isBond_eq>,
> std::random_access_iterator_tag) ()
>    From /home/didges/entroforce/rDock//lib/libRbt.so.rDock
> (gdb) where
> #0 0x00007ffff7e26705 in __gnu_cxx::__normal_iterator<SmartPtr<RbtBond>*,
> std::vector<SmartPtr<RbtBond>, std::allocator<SmartPtr<RbtBond> > > std::
> __find_if<__gnu_cxx::__normal_iterator<SmartPtr<RbtBond>*,
> std::vector<SmartPtr<RbtBond>, std::allocator<SmartPtr<RbtBond> > >,
> __gnu_cxx::__ops::_Iter_pred<Rbt:: isBond_eq>
> >(__gnu_cxx::__normal_iterator<SmartPtr<RbtBond>*,
> std::vector<SmartPtr<RbtBond>, std::allocator<SmartPtr<RbtBond> > >,
> __gnu_cxx::__normal_iterator<SmartPtr<RbtBond>*, std:
> :vector<SmartPtr<RbtBond>, std::allocator<SmartPtr<RbtBond> > >,
> __gnu_cxx::__ops::_Iter_pred<Rbt::isBond_eq>,
> std::random_access_iterator_tag) ()
>    from /home/didges/entroforce/rDock//lib/libRbt.so.rDock
> #1 0x00007ff7e241cf in
> RbtBaseMolecularFileSource::RemoveAtom(SmartPtr<RbtAtom>) () from
> /home/didges/entroforce/rDock/lib/libRbt.so.rDock
> #2 0x00007ff7e9563a in RbtMOL2FileSource::RemoveNonPolarHydrogens() ()
> from /home/didges/entroforce/rDock/lib/libRbt.so.rDock
> #3 0x00007ff7e98000 in RbtMOL2FileSource::SetupAtomParams() () from
> /home/didges/entroforce/rDock/lib/libRbt.so.rDock
> #4 0x00007ff7e99cf3 in RbtMOL2FileSource::Parse() () from
> /home/didges/entroforce/rDock/lib/libRbt.so.rDock
> #5 0x00007ff7e17789 in RbtBaseFileSource::Status() () from
> /home/didges/entroforce/rDock/lib/libRbt.so.rDock
> #6 0x00007ff7ed0a6b in
> RbtPRMFactory::CreateMolFileSource(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&) ()
>    from /home/didges/entroforce/rDock//lib/libRbt.so
> #7 0x00007ff7ed2069 in RbtPRMFactory::CreateReceptor() () from
> /home/didges/entroforce/rDock/lib/libRbt.so.rDock
> #8 0x000055555555c953 in main ()
> (gdb) Segmentation fault
> [9]+ Stopped gdb --args rbdock -i actives_final.sdf -o rdock_out -r
> sys_def.prm -p dock.prm
>
> Thanks in advance,
> Poplavskiy Ivan
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>