rdock-list-def — General Mailing List for rDock users

[rDock-list-def] Some general questions from a newbie

[Callan R. <sup...@ho...>]

Hi all,

Please forgive my basic questions - unfortunately I could not find clear answers from looking in the manual.

First off, when I am comparing docking poses, should I be focussing on <SCORE> or <SCORE.INTER>? The manual states "S Inter is the main term of interest as it represents the protein-ligand (or RNA-ligand) interaction score", but when I brought this up with my project supervisor he assured me to just use total score. I am still unsure of this based on some of the results I have generated.

Secondly, are these score values representative of free binding energy, as with some other programs? If so, are they given in kJ/mol or kCal/mol? Searching the manual for these units did not seem to yield any clear statement of one or the other, but both appeared in the document so I can't make any assumptions.

Thanks so much for your time!
Cal

[rDock-list-def] Fwd: Pose Re Scoring

[Scott B. <sbe...@de...>]

Which routine would allow me to rigid Dock my own conformations?


On Sat, Feb 4, 2023 at 4:12 AM Sergio Ruiz Carmona <sru...@gm...>
wrote:

> Hi Scott,
>
> If you use "score.prm" instead of "dock.prm" when executing rdock, it will
> only score your poses without modifying their coordinates.
> Thanks,
>
> Sergio
>
>
> On Sat, 4 Feb 2023, 22:12 Scott Bembenek, <sbe...@de...>
> wrote:
>
>> Hi All,
>>
>> Is it possible to have rDock simply rescore a given set of poses as they
>> appear in the SDF file?
>>
>> thanks,
>>
>> Scott
>>
> _______________________________________________
>> rDock-list-def mailing list
>> rDo...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>>
>

Re: [rDock-list-def] issues in installing rDock

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

Hi Andriy,

Please refer to https://github.com/CBDD/rDock, as the project has been
ported to GitHub and the installation steps modified.
Hope that helps.
Thanks,

Sergio

On Sat, 16 Dec 2023 at 18:06, Andriy Kovalenko <an...@ua...> wrote:

> Hello,
>
> I downloaded and started installing rDock on my Ubuntu desktop.
> Unfortunately, it interrupted with an error message - please see (1)
> below, highlighted in bold.
>
> Due to message (1), I then started installing *lpopt*.
> However, it ended up again with an error message - please see (2) below,
> highlighted in bold.
>
> Would you please help me out to resolve this issue.
>
> Sincerely,
>
>
> Dr. Andriy Kovalenko
>
> Research Assistant
> Department of Biological Sciences
> University of Alberta
> CW 405, Biological Sciences Bldg.
> Edmonton, Alberta, Canada T6G 2E9
>
> Tel:  780-940-7477 (cell)
> e-mail:  and...@ua...
>
>
> (1) andriy@andriy-Precision-Tower-5810:~/rDock-main$ *sudo make install*
> make lib
> make[1]: Entering directory '/home/andriy/rDock-main'
> g++ -Werror -pipe -std=c++14 -fPIC -O3 -ffast-math   -D_NDEBUG -shared
> -L./lib obj/RbtTriposAtomType.o obj/RbtMdlFileSink.o
> obj/RbtBaseMolecularFileSink.o obj/RbtPdbFileSource.o obj/RbtBaseIntraSF.o
> obj/RbtFilter.o obj/RbtSubject.o obj/RbtEuler.o obj/RbtPMFDirSource.o
> obj/RbtPrincipalAxes.o obj/RbtCellTokenIter.o obj/RbtDihedralTargetSF.o
> obj/RbtGATransform.o obj/RbtChromDihedralRefData.o
> obj/RbtBaseMolecularFileSource.o obj/RbtRotSF.o obj/RbtFlexAtomFactory.o
> obj/RbtNullTransform.o obj/RbtChrom.o obj/RbtSFAgg.o obj/RbtBond.o
> obj/RbtBiMolWorkSpace.o obj/RbtAtomFuncs.o obj/RbtNonBondedGrid.o
> obj/RbtChromPositionRefData.o obj/RbtAlignTransform.o
> obj/RbtSiteMapperFactory.o obj/RbtObserver.o obj/RbtModelMutator.o
> obj/RbtPsfFileSource.o obj/RbtAromIdxSF.o obj/RbtPolarSF.o
> obj/RbtBaseTransform.o obj/RbtBaseBiMolTransform.o obj/RbtSetupPolarSF.o
> obj/RbtDirectorySource.o obj/RbtPopulation.o obj/RbtCavityFillSF.o
> obj/RbtBaseUniMolTransform.o obj/RbtFilterExpressionVisitor.o
> obj/RbtCharmmTypesFileSource.o obj/RbtConstraint.o obj/RbtMOEGrid.o
> obj/RbtChromFactory.o obj/RbtMOL2FileSource.o obj/RbtNonBondedHHSGrid.o
> obj/RbtChromOccupancyElement.o obj/RbtChromElement.o
> obj/RbtChromPositionElement.o obj/RbtAtom.o obj/RbtTransformAgg.o
> obj/RbtCavityGridSF.o obj/RbtRandLigTransform.o obj/RbtModel.o
> obj/RbtCrdFileSource.o obj/RbtAnnotation.o obj/RbtDihedralSF.o
> obj/RbtSimplexTransform.o obj/RbtParser.o obj/RbtDebug.o obj/RbtPMFIdxSF.o
> obj/RbtElementFileSource.o obj/RbtLigandSiteMapper.o obj/RbtVdwIntraSF.o
> obj/RbtLigandFlexData.o obj/RbtAnnotationHandler.o obj/RbtPseudoAtom.o
> obj/RbtBaseObject.o obj/RbtRandPopTransform.o obj/RbtSetupPMFSF.o
> obj/RbtSolventFlexData.o obj/RbtRealGrid.o obj/RbtReceptorFlexData.o
> obj/RbtSFFactory.o obj/RbtChromDihedralElement.o obj/RbtSetupSASF.o
> obj/RbtNoeRestraint.o obj/RbtPsfFileSink.o obj/RbtSiteMapper.o
> obj/RbtPolarIntraSF.o obj/RbtSATypes.o obj/RbtBaseGrid.o obj/RbtWorkSpace.o
> obj/RbtToken.o obj/RbtSphereSiteMapper.o obj/RbtBaseIdxSF.o
> obj/RbtVdwGridSF.o obj/RbtSimAnnTransform.o obj/RbtContext.o
> obj/RbtPRMFactory.o obj/RbtChromOccupancyRefData.o obj/RbtVdwIdxSF.o
> obj/RbtBaseFileSink.o obj/RbtInteractionGrid.o obj/RbtDihedralIntraSF.o
> obj/RbtPharmaSF.o obj/RbtPMFGridSF.o obj/RbtDockingSite.o
> obj/RbtNmrRestraintFileSource.o obj/RbtRand.o obj/RbtVdwSF.o
> obj/RbtCharmmDataSource.o obj/RbtTransformFactory.o obj/RbtBaseFileSource.o
> obj/Rbt.o obj/RbtPMF.o obj/RbtMdlFileSource.o obj/RbtParamHandler.o
> obj/RbtParameterFileSource.o obj/RbtFFTGrid.o obj/RbtNmrSF.o
> obj/RbtPolarIdxSF.o obj/RbtCrdFileSink.o obj/RbtBaseSF.o
> obj/RbtBaseInterSF.o obj/RbtTetherSF.o obj/RbtStringTokenIter.o
> obj/RbtFilterExpression.o obj/RbtGenome.o obj/RbtConstSF.o obj/RbtSAIdxSF.o
> obj/simplex/NMSearch.o obj/GP/RbtGPChromosome.o obj/GP/RbtGPGenome.o
> obj/GP/RbtGPParser.o obj/GP/RbtGPFFGold.o obj/GP/RbtGPFFSpike.o
> obj/GP/RbtGPFitnessFunction.o obj/GP/RbtGPPopulation.o
> obj/GP/RbtGPFFCrossDock.o obj/GP/RbtGPFFCHK1.o obj/GP/RbtGPFFHSP90.o -o
> lib/libRbt.so -lpopt -lm -lstdc++
>
>
>
>
>
> */usr/bin/ld: cannot find -lpopt: No such file or directorycollect2:
> error: ld returned 1 exit statusmake[1]: *** [Makefile:190: lib/libRbt.so]
> Error 1make[1]: Leaving directory '/home/andriy/rDock-main'make: ***
> [Makefile:133: build_lib] Error 2*
>
> (2) andriy@andriy-Precision-Tower-5810:~/Ipopt$ ./configure
> CXX=g++-11.4.0 CC=gcc-11.4.0 F77=gfortran-11.4.0
> checking build system type... x86_64-pc-linux-gnu
> checking host system type... x86_64-pc-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a race-free mkdir -p... /usr/bin/mkdir -p
> checking for gawk... no
> checking for mawk... mawk
> checking whether make sets $(MAKE)... yes
> checking whether make supports nested variables... yes
> checking whether to enable maintainer-specific portions of Makefiles... no
> checking whether make supports the include directive... yes (GNU style)
> checking whether the C compiler works... no
>
>
> *configure: error: in `/home/andriy/Ipopt':configure: error: C compiler
> cannot create executables*See `config.log' for more details
>
>
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] issues in installing rDock

[Andriy K. <an...@ua...>]

Hello,

I downloaded and started installing rDock on my Ubuntu desktop.
Unfortunately, it interrupted with an error message - please see (1) below,
highlighted in bold.

Due to message (1), I then started installing *lpopt*.
However, it ended up again with an error message - please see (2) below,
highlighted in bold.

Would you please help me out to resolve this issue.

Sincerely,


Dr. Andriy Kovalenko

Research Assistant
Department of Biological Sciences
University of Alberta
CW 405, Biological Sciences Bldg.
Edmonton, Alberta, Canada T6G 2E9

Tel:  780-940-7477 (cell)
e-mail:  and...@ua...


(1) andriy@andriy-Precision-Tower-5810:~/rDock-main$ *sudo make install*
make lib
make[1]: Entering directory '/home/andriy/rDock-main'
g++ -Werror -pipe -std=c++14 -fPIC -O3 -ffast-math   -D_NDEBUG -shared
-L./lib obj/RbtTriposAtomType.o obj/RbtMdlFileSink.o
obj/RbtBaseMolecularFileSink.o obj/RbtPdbFileSource.o obj/RbtBaseIntraSF.o
obj/RbtFilter.o obj/RbtSubject.o obj/RbtEuler.o obj/RbtPMFDirSource.o
obj/RbtPrincipalAxes.o obj/RbtCellTokenIter.o obj/RbtDihedralTargetSF.o
obj/RbtGATransform.o obj/RbtChromDihedralRefData.o
obj/RbtBaseMolecularFileSource.o obj/RbtRotSF.o obj/RbtFlexAtomFactory.o
obj/RbtNullTransform.o obj/RbtChrom.o obj/RbtSFAgg.o obj/RbtBond.o
obj/RbtBiMolWorkSpace.o obj/RbtAtomFuncs.o obj/RbtNonBondedGrid.o
obj/RbtChromPositionRefData.o obj/RbtAlignTransform.o
obj/RbtSiteMapperFactory.o obj/RbtObserver.o obj/RbtModelMutator.o
obj/RbtPsfFileSource.o obj/RbtAromIdxSF.o obj/RbtPolarSF.o
obj/RbtBaseTransform.o obj/RbtBaseBiMolTransform.o obj/RbtSetupPolarSF.o
obj/RbtDirectorySource.o obj/RbtPopulation.o obj/RbtCavityFillSF.o
obj/RbtBaseUniMolTransform.o obj/RbtFilterExpressionVisitor.o
obj/RbtCharmmTypesFileSource.o obj/RbtConstraint.o obj/RbtMOEGrid.o
obj/RbtChromFactory.o obj/RbtMOL2FileSource.o obj/RbtNonBondedHHSGrid.o
obj/RbtChromOccupancyElement.o obj/RbtChromElement.o
obj/RbtChromPositionElement.o obj/RbtAtom.o obj/RbtTransformAgg.o
obj/RbtCavityGridSF.o obj/RbtRandLigTransform.o obj/RbtModel.o
obj/RbtCrdFileSource.o obj/RbtAnnotation.o obj/RbtDihedralSF.o
obj/RbtSimplexTransform.o obj/RbtParser.o obj/RbtDebug.o obj/RbtPMFIdxSF.o
obj/RbtElementFileSource.o obj/RbtLigandSiteMapper.o obj/RbtVdwIntraSF.o
obj/RbtLigandFlexData.o obj/RbtAnnotationHandler.o obj/RbtPseudoAtom.o
obj/RbtBaseObject.o obj/RbtRandPopTransform.o obj/RbtSetupPMFSF.o
obj/RbtSolventFlexData.o obj/RbtRealGrid.o obj/RbtReceptorFlexData.o
obj/RbtSFFactory.o obj/RbtChromDihedralElement.o obj/RbtSetupSASF.o
obj/RbtNoeRestraint.o obj/RbtPsfFileSink.o obj/RbtSiteMapper.o
obj/RbtPolarIntraSF.o obj/RbtSATypes.o obj/RbtBaseGrid.o obj/RbtWorkSpace.o
obj/RbtToken.o obj/RbtSphereSiteMapper.o obj/RbtBaseIdxSF.o
obj/RbtVdwGridSF.o obj/RbtSimAnnTransform.o obj/RbtContext.o
obj/RbtPRMFactory.o obj/RbtChromOccupancyRefData.o obj/RbtVdwIdxSF.o
obj/RbtBaseFileSink.o obj/RbtInteractionGrid.o obj/RbtDihedralIntraSF.o
obj/RbtPharmaSF.o obj/RbtPMFGridSF.o obj/RbtDockingSite.o
obj/RbtNmrRestraintFileSource.o obj/RbtRand.o obj/RbtVdwSF.o
obj/RbtCharmmDataSource.o obj/RbtTransformFactory.o obj/RbtBaseFileSource.o
obj/Rbt.o obj/RbtPMF.o obj/RbtMdlFileSource.o obj/RbtParamHandler.o
obj/RbtParameterFileSource.o obj/RbtFFTGrid.o obj/RbtNmrSF.o
obj/RbtPolarIdxSF.o obj/RbtCrdFileSink.o obj/RbtBaseSF.o
obj/RbtBaseInterSF.o obj/RbtTetherSF.o obj/RbtStringTokenIter.o
obj/RbtFilterExpression.o obj/RbtGenome.o obj/RbtConstSF.o obj/RbtSAIdxSF.o
obj/simplex/NMSearch.o obj/GP/RbtGPChromosome.o obj/GP/RbtGPGenome.o
obj/GP/RbtGPParser.o obj/GP/RbtGPFFGold.o obj/GP/RbtGPFFSpike.o
obj/GP/RbtGPFitnessFunction.o obj/GP/RbtGPPopulation.o
obj/GP/RbtGPFFCrossDock.o obj/GP/RbtGPFFCHK1.o obj/GP/RbtGPFFHSP90.o -o
lib/libRbt.so -lpopt -lm -lstdc++





*/usr/bin/ld: cannot find -lpopt: No such file or directorycollect2: error:
ld returned 1 exit statusmake[1]: *** [Makefile:190: lib/libRbt.so] Error
1make[1]: Leaving directory '/home/andriy/rDock-main'make: ***
[Makefile:133: build_lib] Error 2*

(2) andriy@andriy-Precision-Tower-5810:~/Ipopt$ ./configure CXX=g++-11.4.0
CC=gcc-11.4.0 F77=gfortran-11.4.0
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking whether make supports the include directive... yes (GNU style)
checking whether the C compiler works... no


*configure: error: in `/home/andriy/Ipopt':configure: error: C compiler
cannot create executables*See `config.log' for more details

Re: [rDock-list-def] Pose Re Scoring

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

Hi Scott,

If you use "score.prm" instead of "dock.prm" when executing rdock, it will
only score your poses without modifying their coordinates.
Thanks,

Sergio


On Sat, 4 Feb 2023, 22:12 Scott Bembenek, <sbe...@de...> wrote:

> Hi All,
>
> Is it possible to have rDock simply rescore a given set of poses as they
> appear in the SDF file?
>
> thanks,
>
> Scott
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] Pose Re Scoring

[Scott B. <sbe...@de...>]

Hi All,

Is it possible to have rDock simply rescore a given set of poses as they
appear in the SDF file?

thanks,

Scott

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
>

Re: [rDock-list-def] rdkit installation issues

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

Hi Mandar,

Thanks for your interest on rDock.
Those are known issues and there have been some improvements on the github
repository, I would recommend to try and install one of the dev branches
from source:

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

The conda installation is independent from the rDock team and the
segmentation fault error has been appearing since it was ported, sorry.
Thanks again,

Sergio

On Wed, 20 Apr 2022 at 15:18, Mandar Kulkarni <
man...@gm...> wrote:

> Hello Everyone,
>
> I am trying to install rDOCK on Ubuntu 20.04 (rDock_2013.1_src.tar.gz).
> All the dependencies are installed.
> However, after the *"make *Linux*-g++-64" *command, I am getting the
> following error:
>
> ../import/simplex/src/NMSearch.cxx:391:13: note:   ‘std::istream’ {aka
> ‘std::basic_istream<char>’} is not derived from ‘const std::multiset<_Key,
> _Compare, _Alloc>’
>   391 |    if(fp == NULL) {
>       |             ^~~~
> make[2]: *** [Makefile.linux-g++-64-release-lib:555:
> linux-g++-64/release/obj/RbtGPChromosome.o] Error 1
> make[2]: *** Waiting for unfinished jobs....
> make[2]: *** [Makefile.linux-g++-64-release-lib:552:
> linux-g++-64/release/obj/NMSearch.o] Error 1
> make[2]: *** [Makefile.linux-g++-64-release-lib:561:
> linux-g++-64/release/obj/RbtGPFFCrossDock.o] Error 1
> make[2]: *** [Makefile.linux-g++-64-release-lib:558:
> linux-g++-64/release/obj/RbtGPFFCHK1.o] Error 1
> make[2]: Leaving directory
> '/home/mandar/softwares/rDOCK/rDock_2013.1_src/build'
> make[1]: *** [Makefile:95: rdock-lib] Error 2
> make[1]: Leaving directory
> '/home/mandar/softwares/rDOCK/rDock_2013.1_src/build'
> make: *** [makefile:73: linux-g++-64] Error 2
>
> I am not sure about the origin of this error. Any suggestions would be
> appreciated.
>
> Also, as an alternative, I installed rDOCK with bioconda conda channel.
> The executables are available in the bin/ folder. But, when tried with 1sj0
> of the validation set, I got a segmentation fault.
>
> Command line arguments:
> -r 1sj0_rdock.prm
> -was
> /home/mandar/anaconda3/envs/docking-rdock/bin/rbcavity: line 7: 224720
> Segmentation fault      (core dumped) "$RBT_ROOT/bin/$PROGNAME" "$@"
>
> The variables in the rbcavity script are pointed to the correct file
> location, so again I am not sure what is causing the error.
>
> Do I need to modify tmake.conf before installation?
>
> It will be helpful to receive suggestions or pointers if I am missing
> something here.
>
> Thanks in advance,
> Mandar Kulkarni
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

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

[Ivan P. <pop...@en...>]

<div><div style="background-color:rgb( 255 , 255 , 255 );color:rgb( 0 , 0 , 0 );font-family:'ys text' , 'arial' , sans-serif;font-size:16px;font-style:normal;font-weight:400;text-align:left;text-decoration-style:initial;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Hello Everyone,</div><div style="background-color:rgb( 255 , 255 , 255 );color:rgb( 0 , 0 , 0 );font-family:'ys text' , 'arial' , sans-serif;font-size:16px;font-style:normal;font-weight:400;text-align:left;text-decoration-style:initial;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"> </div><div style="background-color:rgb( 255 , 255 , 255 );color:rgb( 0 , 0 , 0 );font-family:'ys text' , 'arial' , sans-serif;font-size:16px;font-style:normal;font-weight:400;text-align:left;text-decoration-style:initial;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div>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?</div><div>Starting program: /home/didges/entroforce/rDock/bin/rbdock -i actives_final.sdf -o rdock_out -r sys_def.prm -p dock.prm</div><div>***********************************************</div><div>The rDock program is licensed under GNU-LGPLv3.0. <a href="http://rdock.sourceforge.net/" rel="noopener noreferrer" target="_blank">http://rdock.sourceforge.net/</a></div><div>Executable: rbdock ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $)</div><div>Library: libRbt.so/2013.1/901 2013/11/27</div><div>RBT_ROOT: /home/didges/entroforce/rDock/</div><div>RBT_HOME: /home/didges</div><div>Current dir:    /home/didges/entroforce/rdock_tests/ada</div><div>Date:        Wed May 4 15:03:31 2022</div><div>***********************************************</div><div> </div><div>Command line args:</div><div> -i actives_final.sdf</div><div> -r sys_def.prm</div><div> -p dock.prm</div><div> -o rdock_out</div><div> -n 1 (default) </div><div>Reading polar hydrogens only from ligand SD file</div><div> </div><div>DOCKING PROTOCOL:</div><div>dock.prm</div><div> </div><div>RECEPTOR:</div><div>sys_def.prm</div><div>4dfr oxido-reductase</div><div> </div><div>DOCKING SITE</div><div>Total volume 509.5 A^3</div><div>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)</div><div> </div><div>Program received signal SIGSEGV, Segmentation fault.</div><div> </div><div>gdb gave this result:</div><div> </div><div>0x00007ffff7e26705 in __gnu_cxx::__normal_iterator&lt;SmartPtr&lt;RbtBond&gt;*, std::vector&lt;SmartPtr&lt;RbtBond&gt;, std::allocator&lt;SmartPtr&lt;RbtBond&gt; &gt; &gt; std::__find_if&lt;__gnu_cxx: :__normal_iterator&lt;SmartPtr&lt;RbtBond&gt;&gt;*, std::vector&lt;SmartPtr&lt;RbtBond&gt;, std::allocator&lt;SmartPtr&lt;RbtBond&gt; &gt; &gt;, __gnu_cxx::__ops::_Iter_pred&lt;Rbt::isBond_eq&gt; &gt;(__gnu_cxx: :__normal_iterator&lt;SmartPtr&lt;RbtBond&gt;&gt;*, std::vector&lt;SmartPtr&lt;RbtBond&gt;, std::allocator&lt;SmartPtr&lt;RbtBond&gt; &gt; &gt;, __gnu_cxx::__normal_iterator&lt;SmartPtr&lt;RbtBond&gt;*, std: :vector&lt;SmartPtr&lt;RbtBond&gt;, std::allocator&lt;SmartPtr&lt;RbtBond&gt; &gt; &gt;, __gnu_cxx::__ops::_Iter_pred&lt;Rbt::isBond_eq&gt;, std::random_access_iterator_tag) ()</div><div>   From /home/didges/entroforce/rDock//lib/libRbt.so.rDock</div><div>(gdb) where</div><div>#0 0x00007ffff7e26705 in __gnu_cxx::__normal_iterator&lt;SmartPtr&lt;RbtBond&gt;*, std::vector&lt;SmartPtr&lt;RbtBond&gt;, std::allocator&lt;SmartPtr&lt;RbtBond&gt; &gt; &gt; std:: __find_if&lt;__gnu_cxx::__normal_iterator&lt;SmartPtr&lt;RbtBond&gt;*, std::vector&lt;SmartPtr&lt;RbtBond&gt;, std::allocator&lt;SmartPtr&lt;RbtBond&gt; &gt; &gt;, __gnu_cxx::__ops::_Iter_pred&lt;Rbt:: isBond_eq&gt; &gt;(__gnu_cxx::__normal_iterator&lt;SmartPtr&lt;RbtBond&gt;*, std::vector&lt;SmartPtr&lt;RbtBond&gt;, std::allocator&lt;SmartPtr&lt;RbtBond&gt; &gt; &gt;, __gnu_cxx::__normal_iterator&lt;SmartPtr&lt;RbtBond&gt;*, std: :vector&lt;SmartPtr&lt;RbtBond&gt;, std::allocator&lt;SmartPtr&lt;RbtBond&gt; &gt; &gt;, __gnu_cxx::__ops::_Iter_pred&lt;Rbt::isBond_eq&gt;, std::random_access_iterator_tag) ()</div><div>   from /home/didges/entroforce/rDock//lib/libRbt.so.rDock</div><div>#1 0x00007ff7e241cf in RbtBaseMolecularFileSource::RemoveAtom(SmartPtr&lt;RbtAtom&gt;) () from /home/didges/entroforce/rDock/lib/libRbt.so.rDock</div><div>#2 0x00007ff7e9563a in RbtMOL2FileSource::RemoveNonPolarHydrogens() () from /home/didges/entroforce/rDock/lib/libRbt.so.rDock</div><div>#3 0x00007ff7e98000 in RbtMOL2FileSource::SetupAtomParams() () from /home/didges/entroforce/rDock/lib/libRbt.so.rDock</div><div>#4 0x00007ff7e99cf3 in RbtMOL2FileSource::Parse() () from /home/didges/entroforce/rDock/lib/libRbt.so.rDock</div><div>#5 0x00007ff7e17789 in RbtBaseFileSource::Status() () from /home/didges/entroforce/rDock/lib/libRbt.so.rDock</div><div>#6 0x00007ff7ed0a6b in RbtPRMFactory::CreateMolFileSource(std::__cxx11::basic_string&lt;char, std::char_traits&lt;char&gt;, std::allocator&lt;char&gt; &gt; const&amp;) ()</div><div>   from /home/didges/entroforce/rDock//lib/libRbt.so</div><div>#7 0x00007ff7ed2069 in RbtPRMFactory::CreateReceptor() () from /home/didges/entroforce/rDock/lib/libRbt.so.rDock</div><div>#8 0x000055555555c953 in main ()</div><div>(gdb) Segmentation fault</div><div>[9]+ Stopped gdb --args rbdock -i actives_final.sdf -o rdock_out -r sys_def.prm -p dock.prm</div><div> </div><div>Thanks in advance,</div><div>Poplavskiy Ivan</div></div></div>

[rDock-list-def] rdkit installation issues

[Mandar K. <man...@gm...>]

Hello Everyone,

I am trying to install rDOCK on Ubuntu 20.04 (rDock_2013.1_src.tar.gz). All
the dependencies are installed.
However, after the *"make *Linux*-g++-64" *command, I am getting the
following error:

../import/simplex/src/NMSearch.cxx:391:13: note:   ‘std::istream’ {aka
‘std::basic_istream<char>’} is not derived from ‘const std::multiset<_Key,
_Compare, _Alloc>’
  391 |    if(fp == NULL) {
      |             ^~~~
make[2]: *** [Makefile.linux-g++-64-release-lib:555:
linux-g++-64/release/obj/RbtGPChromosome.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: *** [Makefile.linux-g++-64-release-lib:552:
linux-g++-64/release/obj/NMSearch.o] Error 1
make[2]: *** [Makefile.linux-g++-64-release-lib:561:
linux-g++-64/release/obj/RbtGPFFCrossDock.o] Error 1
make[2]: *** [Makefile.linux-g++-64-release-lib:558:
linux-g++-64/release/obj/RbtGPFFCHK1.o] Error 1
make[2]: Leaving directory
'/home/mandar/softwares/rDOCK/rDock_2013.1_src/build'
make[1]: *** [Makefile:95: rdock-lib] Error 2
make[1]: Leaving directory
'/home/mandar/softwares/rDOCK/rDock_2013.1_src/build'
make: *** [makefile:73: linux-g++-64] Error 2

I am not sure about the origin of this error. Any suggestions would be
appreciated.

Also, as an alternative, I installed rDOCK with bioconda conda channel. The
executables are available in the bin/ folder. But, when tried with 1sj0 of
the validation set, I got a segmentation fault.

Command line arguments:
-r 1sj0_rdock.prm
-was
/home/mandar/anaconda3/envs/docking-rdock/bin/rbcavity: line 7: 224720
Segmentation fault      (core dumped) "$RBT_ROOT/bin/$PROGNAME" "$@"

The variables in the rbcavity script are pointed to the correct file
location, so again I am not sure what is causing the error.

Do I need to modify tmake.conf before installation?

It will be helpful to receive suggestions or pointers if I am missing
something here.

Thanks in advance,
Mandar Kulkarni

Re: [rDock-list-def] H donor center in pharmacophores constraint

[Tim D. <tdu...@gm...>]

I believe it's the heavy atom.

On Fri, Oct 15, 2021 at 3:04 AM Shi, Xuetao <xue...@uc...> wrote:

> Hi,
>
> I am running some rDock calculations with pharmacophore constraints. One
> of such constraints is the hydrogen donor of hydrogen bonding. Does anyone
> know if the center coordinate of this constraint should be placed at the
> hydrogen atom or the heavy atom? Thank you very much!
>
>
>
> Best,
>
> Xuetao
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

Re: [rDock-list-def] compiling with newer compilers

[Peter S. <pet...@di...>]

Cool! thanks a lot!!

Peter

________________________________
From: Sergio Ruiz <sru...@gm...>
Sent: Thursday, November 4, 2021 02:58
To: Peter Schmidtke <pet...@di...>
Cc: rdo...@li... <rdo...@li...>
Subject: Re: [rDock-list-def] compiling with newer compilers

Hi Peter,

I encountered the same frustrating error a while ago when also trying to compile with newer compilers.
I spent some time finding a solution and you can find it here:

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

I have not had the time to properly validate it (that's why it's not been merged to the main branch) but it has been compiling and running for me with no issues and same results as the "older" compiler version.
Let me know if it does not work for you!
Best,

Sergi

---------- Forwarded message ----------
From: Peter Schmidtke <pet...@di...<mailto:pet...@di...>>
To: "rdo...@li...<mailto:rdo...@li...>" <rdo...@li...<mailto:rdo...@li...>>
Cc:
Bcc:
Date: Wed, 3 Nov 2021 14:06:29 +0000
Subject: compiling with newer compilers
Hi all,

I'm currently trying to make the necessary changes to be able to compile rdock with newer compilers.

First of all the basic make thing doesn"t seem to work (in srcforge & github repo), but found my way around that for now.
I have this error on execution:

RBT_FILE_MISSING_PARAMETER at ../src/lib/RbtParameterFileSource.cxx, line 84
GLU:: parameter not found in /rDock_2013.1_src/data/sf/RbtIonicAtoms.prm

on this command line:

/rDock_2013.1_src/build/test/RBT_HOME# rbcavity -r 1YET.prm
***********************************************
The rDock program is licensed under GNU-LGPLv3.0. http://rdock.sourceforge.net/
Executable:     rbcavity ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbcavity.cxx#3 $)
Library:        libRbt.so/2013.1/901 2013/11/27
RBT_ROOT:       /rDock_2013.1_src
RBT_HOME:       /root
Current dir:    /rDock_2013.1_src/build/test/RBT_HOME
Date:           Wed Nov  3 13:53:44 2021
***********************************************

Command line arguments:
-r 1YET.prm


I looked like a env variable misconfiguration to me, but checked vs working envs and there's no difference.

Did anybody experience this issue before?

Cheers

Peter

Re: [rDock-list-def] compiling with newer compilers

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

Hi Peter,

I encountered the same frustrating error a while ago when also trying to
compile with newer compilers.
I spent some time finding a solution and you can find it here:

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

I have not had the time to properly validate it (that's why it's not been
merged to the main branch) but it has been compiling and running for me
with no issues and same results as the "older" compiler version.
Let me know if it does not work for you!
Best,

Sergi

---------- Forwarded message ----------
From: Peter Schmidtke <pet...@di...>
To: "rdo...@li..." <
rdo...@li...>
Cc:
Bcc:
Date: Wed, 3 Nov 2021 14:06:29 +0000
Subject: compiling with newer compilers
Hi all,

I'm currently trying to make the necessary changes to be able to compile
rdock with newer compilers.

First of all the basic make thing doesn"t seem to work (in srcforge &
github repo), but found my way around that for now.
I have this error on execution:

RBT_FILE_MISSING_PARAMETER at ../src/lib/RbtParameterFileSource.cxx, line 84
GLU:: parameter not found in /rDock_2013.1_src/data/sf/RbtIonicAtoms.prm

on this command line:

/rDock_2013.1_src/build/test/RBT_HOME# rbcavity -r 1YET.prm
***********************************************
The rDock program is licensed under GNU-LGPLv3.0.
http://rdock.sourceforge.net/
Executable:     rbcavity ($Id:
//depot/dev/client3/rdock/2013.1/src/exe/rbcavity.cxx#3 $)
Library:        libRbt.so/2013.1/901 2013/11/27
RBT_ROOT:       /rDock_2013.1_src
RBT_HOME:       /root
Current dir:    /rDock_2013.1_src/build/test/RBT_HOME
Date:           Wed Nov  3 13:53:44 2021
***********************************************

Command line arguments:
-r 1YET.prm


I looked like a env variable misconfiguration to me, but checked vs working
envs and there's no difference.

Did anybody experience this issue before?

Cheers

Peter

[rDock-list-def] compiling with newer compilers

[Peter S. <pet...@di...>]

Hi all,

I'm currently trying to make the necessary changes to be able to compile rdock with newer compilers.

First of all the basic make thing doesn"t seem to work (in srcforge & github repo), but found my way around that for now.
I have this error on execution:

RBT_FILE_MISSING_PARAMETER at ../src/lib/RbtParameterFileSource.cxx, line 84
GLU:: parameter not found in /rDock_2013.1_src/data/sf/RbtIonicAtoms.prm

on this command line:

/rDock_2013.1_src/build/test/RBT_HOME# rbcavity -r 1YET.prm
***********************************************
The rDock program is licensed under GNU-LGPLv3.0. http://rdock.sourceforge.net/
Executable:     rbcavity ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbcavity.cxx#3 $)
Library:        libRbt.so/2013.1/901 2013/11/27
RBT_ROOT:       /rDock_2013.1_src
RBT_HOME:       /root
Current dir:    /rDock_2013.1_src/build/test/RBT_HOME
Date:           Wed Nov  3 13:53:44 2021
***********************************************

Command line arguments:
-r 1YET.prm


I looked like a env variable misconfiguration to me, but checked vs working envs and there's no difference.

Did anybody experience this issue before?

Cheers

Peter

[rDock-list-def] H donor center in pharmacophores constraint

[Shi, X. <xue...@uc...>]

Hi,
I am running some rDock calculations with pharmacophore constraints. One of such constraints is the hydrogen donor of hydrogen bonding. Does anyone know if the center coordinate of this constraint should be placed at the hydrogen atom or the heavy atom? Thank you very much!

Best,
Xuetao

Re: [rDock-list-def] Grid Size

[Markus M. <me...@gm...>]

Scott:
Have you checked chapter 8.4 in the user manual?
Best,
Markus

On Fri, Sep 24, 2021 at 9:10 PM Scott Bembenek <sbe...@de...>
wrote:

> Is there way to define the x,y,x dimensions & center of the grid manually?--
>
> Scott Bembenek, Founder, CEO, CSO
> Denovicon Therapeutics <https://www.denovicontx.com/>
> 1130 Wall St #558
> La Jolla, CA 92037
> <https://www.denovicontx.com/>
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] Grid Size

[Scott B. <sbe...@de...>]

Is there way to define the x,y,x dimensions & center of the grid manually?--

Scott Bembenek, Founder, CEO, CSO
Denovicon Therapeutics <https://www.denovicontx.com/>
1130 Wall St #558
La Jolla, CA 92037
<https://www.denovicontx.com/>

[rDock-list-def] Grid Size

[Scott B. <sbe...@gm...>]

Is there way to define the x,y,x dimensions & center of the grid manually?

Re: [rDock-list-def] Docking of small ligand to protein/RNA receptor

[Markus M. <me...@gm...>]

Dear Line:
I have not tried this but it should work in principle. Just ensure protein and rna are in the receptor file. May be you can try and report your experience?
Good luck,
Markus

> On Mar 23, 2021, at 3:05 AM, Line Abildgaard Ryberg <lin...@su...> wrote:
> 
> 
> Dear users,
> 
> I am a new user of rDock. I would like to dock a small ligands to a receptor consisting of both RNA and protein. Thus, the ligand interacts both with the RNA and the protein. Is this possible with rDock or is it meant for either small molecule-RNA or small molecule-protein?
> 
> Thank you very much.
> 
> Best regards
> Line
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def

[rDock-list-def] Docking of small ligand to protein/RNA receptor

[Line A. R. <lin...@su...>]

Dear users,

I am a new user of rDock. I would like to dock a small ligands to a receptor consisting of both RNA and protein. Thus, the ligand interacts both with the RNA and the protein. Is this possible with rDock or is it meant for either small molecule-RNA or small molecule-protein?

Thank you very much.

Best regards
Line

[rDock-list-def] meaning of score

[Lalehan O. <lal...@gm...>]

Hello,

I followed HTVS protocol as mentioned here:
http://rdock.sourceforge.net/multistep-protocol-for-htvs/

However, I assumed the score there refers to SCORE,INTER, as it has to
represent the binding energy of the ligand? Unless I'm wrong.

Thanks in advance for any insight.

Lalehan

[rDock-list-def] bash: syntax error

[Lalehan O. <lal...@gm...>]

Hello everyone,
When I try to run splitted sd files as instructed here:
http://rdock.sourceforge.net/how-to-run-rdock-in-parallel/

and run the command below:
for file in split*sd do rbdock -i $file -o ${file%%.*}_out -r
mpges_rdock.prm -p dock.prm -n 50 & done

I get this error: "-bash: syntax error near unexpected token `;'  "

Any help would be appreciated.

Lalehan

Re: [rDock-list-def] rDock Compilation issues

[Scott B. <sbe...@de...>]

Perhaps try the docker install:

https://hub.docker.com/r/informaticsmatters/rdock

Or get the newest version, RxDock:

https://www.rxdock.org/

Scott


On Tue, Feb 16, 2021 at 1:37 PM Siddharth Gilra <sid...@gm...>
wrote:

> Hi,
>
> I am having trouble with the make linux-g++-64 command. I always get a
> bunch of errors being shown. I have tried typing the make test command as
> well after, but then it says to type the linux-g++-64 command again. I need
> help with the installation please
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] rDock Compilation issues

[Siddharth G. <sid...@gm...>]

Hi,

I am having trouble with the make linux-g++-64 command. I always get a
bunch of errors being shown. I have tried typing the make test command as
well after, but then it says to type the linux-g++-64 command again. I need
help with the installation please

[rDock-list-def] Grid File

[Scott B. <sbe...@de...>]

Is the .grd file only needed to visualize the grid? In other words, it's
not actually needed for the rdock run -- correct?

thanks,

Scott

Scott Bembenek, Founder, CEO, CSO
Denovicon Therapeutics <https://www.denovicontx.com/>
1130 Wall St #558
La Jolla, CA 92037
<https://www.denovicontx.com/>