When performing docking with RXDock using the same input across different operating systems, I noticed that the results vary. Specifically, I tested on the following environments:
Ubuntu (AMD) CentOS (Intel) Mac (ARM-64) In all cases, the seed was consistently set to 1. Despite this, the docking results were not identical.
Is this behavior expected? If so, could you clarify what might cause such differences? Additionally, are there any recommendations for ensuring consistent results across different OS and hardware configurations?
Thank you.
Thank you so much for this suggestion: 10<RADIUS<20 - I think this is the reason why the code has been so slow for me. I will try to keep it within this range and resolve this.
Weird though.In another section of the reference guide(https://rxdock.gitlab.io/documentation/devel/html/reference-guide/system-definition-file.html#sdf-cavity-mapping),the default large sphere redius is 4 A.
In its source code(https://gitlab.com/rxdock/rxdock/-/blob/master/lib/SphereSiteMapper.cxx?ref_type=heads)line 41,4A is the default.
Also,it's recommended that 10<RADIUS<20.Maybe the RADIUS is so big that it effects the performance.
Hope this helps you.
Hi. Thanks for the reply. I am using the default large sphere radius only (6 Angstroms) and the small sphere radius is also the default value (1.5 Angstroms). I am only modifying the RADIUS parameter of the .prm file to the maximum euclidean distance observed between all pairs of atoms in the RNA structure. In the reference guide (https://rxdock.gitlab.io/documentation/devel/html/reference-guide/cavity-mapping.html#two-sphere-method), it has been mentioned that a grid is set with radius=RADIUS and center=CENTER from the .prm file. I am altering this RADIUS to the maximum euclidean distance and CENTER to the centre of geometry of the RNA structure. I did this so that the entire structure is part of the search grid of the program. The large and small sphere radii are kept at their default values.
Using the default large sphere redius is enough.Too large redius makes the large sphere meaningless.
Dear team,
I have been trying to use rbcavity as a RNA-specific pocket prediction method, to identify all possible cavities in an RNA structure. When the RNA structure is large (more than 100 nucleotides), I find that rbcavity takes very long time to complete writing the .grd files. For example, for PDB ID: 4FAW, I got 8 cavities using the two sphere method, with the radius set to cover the entire RNA. The program has been running for past 1 hour and is yet to complete writing the .grd files for the 8 cavities. I am using Ubuntu 22.04.5 LTS in an 8 core CPU machine. I faced similar issue with another machine as well for the same RNA - Ubuntu 22.04.5 LTS and with 16 cores. How can I make rbcavity faster for larger structures? Is there any specific memory requirement to run the program? Your suggestions will be very helpful for me to use the program for my current project.
With regards, Sowmya
The first line of 6TRX-6TRX.prm is RBT_PARAMETER_FILE_V1.00 instead of RBT PARAMETER_FILE_V1.00.
Good luck.
Hi. Maybe someone has occured the same problem. I am gonna to run docking with RxDock (installed via bioconda), but there is a problem.
RxDock is maintained by Vedran Miletić, Patrik Nikolić, and Luka Vretenar.
Visit https://www.rxdock.org/ for more information.
Executable: rbdock/0.1.0
Library: librxdock.so/0.1.0
RBT_ROOT: /mnt/raid/mwisniewski/conda/abyss/share/rxdock-2013.1.1_148c5bd1-1
RBT_HOME: /mnt/raid/mwisniewski/PhD/data
Current dir: /mnt/raid/mwisniewski/PhD/script
Date: Wed Dec 6 10:28:36 2023
***********************************************
Command line args:
-i /mnt/raid/mwisniewski/PhD/data/bdb2020plus/ligand/sdf/6TRX_ligand.sdf
-r /mnt/raid/mwisniewski/PhD/data/bdb2020plus/docs/temp/6TRX-6TRX.prm
-p dock.prm
-o /mnt/raid/mwisniewski/PhD/data/bdb2020plus/docs/6TRX-6TRX
-n 100
Reading polar hydrogens only from ligand SD file
DOCKING PROTOCOL:
/mnt/raid/mwisniewski/conda/abyss/share/rxdock-2013.1.1_148c5bd1-1/data/scripts/dock.prm
Free docking (indexed VDW)
RECEPTOR:
/mnt/raid/mwisniewski/PhD/data/bdb2020plus/docs/temp/6TRX-6TRX.prm
RBT_FILE_PARSE_ERROR at ../src/lib/RbtParameterFileSource.cxx, line 162
Missing RBT_PARAMETER_FILE_V1.00 string in /mnt/raid/mwisniewski/PhD/data/bdb2020plus/docs/temp/6TRX-6TRX.prm
Have you ever had this kind of problem? prm, mol2 and sdf files are attached.
Maciek
A dirty way:
meson -Dbuildtype=release -Dtests=false some-xxx-builddir
I'm not sure why it is wrong,maybe gtest's system path changes too.
okay, problem again. currently with googletest so, I've got installed good version of google test (apt list --installed):
googletest/focal,focal,now 1.10.0-2 all [installed]
but after typing meson command, this output line is shown:
Run-time dependency GTest found: YES 1.14.0
and later in ninja, errors occures.
(Former) maintainer here.
RxDock is mostly unmaintained since early 2022 and the dismantling of RxTx by Patrik and myself. Over the last year and a half, I have only integrated patches by others and rebuilt the Sphinx docs several times to avoid serving obsolete/insecure JavaScript library versions.
As for the tool itself, newer versions of Eigen, {fmt}, and possibly other libraries are incompatibile. For various reasons, I have no time to devote to the project for the foreseeable future. It would be great if RxDock could get a new maintainer that would keep it updated with the evolution of software.
If there is interest in taking over maintenance of RxDock by one or more active community members, I would gladly consider it.
(Former) maintainer here.
Indeed, this is true, RxDock is mostly unmaintained since early 2022 and the dismantling of RxTx by Patrik and myself. I have only integrated patches by others and rebuilt the Sphinx docs several times to avoid serving obsolete/insecure JavaScript library versions.
As for the tool itself, Eigen incompatibility is unfortunately far from the only problem with the code. I tried compiling it several months ago and got errors with the new version of {fmt}. Rough estimate has shown that it would take several hours of work to adapt it to the new API. There might be more luck (and therefore less work) with adapting to new Eigen, I haven't looked into it.
At some point I might take time to write down the history of RxDock's three years that we worked on it and explain how (and why) we ended our involvement. There are both professional and personal reasons for this decision on my and Patrik's side. For now, it is enough to say that I am unlikely to find time to perform any code changes for the next few years (and Patrik wasn't a developer anyway).
If there is interest in taking over maintenance of RxDock by one or more active community members, I would gladly consider it.
Rxdock didn't update for some time.
Your eigen is too new for rxdock.
Try to install libeigen3-dev 3.3.7 version according to the official install guide.
yes, it helped a little, but after i moved eigens' library into its parent path, following things occured:rxdock.log
Yes.
Install eigen library first.
Usually,you also need to move eigens' library directory into its parent path.
It's a common problem when using cmake and eigen.I don't have computers nearby,but I'm sure there are lots of the same problem and solutions from search engines.
Hi,
while installing the program, I occured the following problem (logs below). Additionally, it adds information about my env and system:
Ubuntu 20.04.6 LTS
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
meson 0.53.2
cmake version 3.25.2
pkg-config 0.29.1
libfmt-dev/focal,now 6.1.2+ds-2
libeigen3-dev/focal,focal,now 3.3.7-2
libpcg-cpp-dev/focal,focal,now 0.98.1-2
googletest/focal,focal,now 1.10.0-2Has anyone ever had such a problem?
$ meson -Dbuildtype=release -Dtests=true builddir
The Meson build system
Version: 0.53.2
Source dir: /mnt/raid/mwisniewski/software/docking/rxdock
Build dir: /mnt/raid/mwisniewski/software/docking/rxdock/builddir
Build type: native build
Project name: RxDock
Project version: 0.1.0
C++ compiler for the host machine:
c++ (gcc 9.4.0 "c++ (Ubuntu 9.4.0-1ubuntu1\~20.04.2) 9.4.0")
C++ linker for the host machine: c++ ld.bfd 2.34
Host machine cpu family: x86_64
Host machine cpu: x86_64
Found pkg-config: /usr/bin/pkg-config (0.29.1)
Run-time dependency eigen3 found: YES 3.3.7
Run-time dependency OpenMP found: YES 4.5
Run-time dependency pcg-cpp found: YES 0.98.1
Run-time dependency cxxopts found: YES 2.2.1
Found CMake: /usr/bin/cmake (3.25.2)
Run-time dependency dt_smarts found: NO (tried pkgconfig and cmake)
Run-time dependency dt_smiles found: NO (tried pkgconfig and cmake)
Run-time dependency GTest found: YES 1.14.0 Build targets in project: 9
Found ninja-1.10.0 at /usr/bin/ninjaproblem
$ ninja -C builddir
ninja: Entering directory `builddir'
[1/145] Compiling C++ object 'rxdock@sha/src_GP_RbtGPFFCrossDock.cxx.o'.
FAILED: rxdock@sha/src_GP_RbtGPFFCrossDock.cxx.o
c++ -Irxdock@sha -I. -I.. -I../include -I../include/GP -I/usr/local/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++11 -O3 -fPIC -fopenmp -MD -MQ 'rxdock@sha/src_GP_RbtGPFFCrossDock.cxx.o' -MF 'rxdock@sha/src_GP_RbtGPFFCrossDock.cxx.o.d' -o 'rxdock@sha/src_GP_RbtGPFFCrossDock.cxx.o' -c ../src/GP/RbtGPFFCrossDock.cxx
In file included from ../include/RbtCavity.h:22,
from ../include/RbtDockingSite.h:23,
from ../include/RbtContext.h:21,
from ../include/GP/RbtGPFitnessFunction.h:19,
from ../include/GP/RbtGPFFCrossDock.h:19,
from ../src/GP/RbtGPFFCrossDock.cxx:13:
../include/RbtRealGrid.h:24:10: fatal error: unsupported/Eigen/CXX11/Tensor: No such file or directory
24 | #include <unsupported/Eigen/CXX11/Tensor>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[2/145] Compiling C++ object 'rxdock@sha/src_GP_RbtGPFFCHK1.cxx.o'.
FAILED: rxdock@sha/src_GP_RbtGPFFCHK1.cxx.o
c++ -Irxdock@sha -I. -I.. -I../include -I../include/GP -I/usr/local/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++11 -O3 -fPIC -fopenmp -MD -MQ 'rxdock@sha/src_GP_RbtGPFFCHK1.cxx.o' -MF 'rxdock@sha/src_GP_RbtGPFFCHK1.cxx.o.d' -o 'rxdock@sha/src_GP_RbtGPFFCHK1.cxx.o' -c ../src/GP/RbtGPFFCHK1.cxx
In file included from ../include/RbtCavity.h:22,
from ../include/RbtDockingSite.h:23,
from ../include/RbtContext.h:21,
from ../include/GP/RbtGPFFCHK1.h:19,
from ../src/GP/RbtGPFFCHK1.cxx:13:
../include/RbtRealGrid.h:24:10: fatal error: unsupported/Eigen/CXX11/Tensor: No such file or directory
24 | #include <unsupported/Eigen/CXX11/Tensor>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[3/145] Compiling C++ object 'rxdock@sha/src_GP_RbtGPFitnessFunction.cxx.o'.
FAILED: rxdock@sha/src_GP_RbtGPFitnessFunction.cxx.o
c++ -Irxdock@sha -I. -I.. -I../include -I../include/GP -I/usr/local/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++11 -O3 -fPIC -fopenmp -MD -MQ 'rxdock@sha/src_GP_RbtGPFitnessFunction.cxx.o' -MF 'rxdock@sha/src_GP_RbtGPFitnessFunction.cxx.o.d' -o 'rxdock@sha/src_GP_RbtGPFitnessFunction.cxx.o' -c ../src/GP/RbtGPFitnessFunction.cxx
In file included from ../include/RbtCavity.h:22,
from ../include/RbtDockingSite.h:23,
from ../include/RbtContext.h:21,
from ../include/GP/RbtGPFitnessFunction.h:19,
from ../src/GP/RbtGPFitnessFunction.cxx:13:
../include/RbtRealGrid.h:24:10: fatal error: unsupported/Eigen/CXX11/Tensor: No such file or directory
24 | #include <unsupported/Eigen/CXX11/Tensor>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[4/145] Compiling C++ object 'rxdock@sha/src_GP_RbtGPFFSpike.cxx.o'.
FAILED: rxdock@sha/src_GP_RbtGPFFSpike.cxx.o
c++ -Irxdock@sha -I. -I.. -I../include -I../include/GP -I/usr/local/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++11 -O3 -fPIC -fopenmp -MD -MQ 'rxdock@sha/src_GP_RbtGPFFSpike.cxx.o' -MF 'rxdock@sha/src_GP_RbtGPFFSpike.cxx.o.d' -o 'rxdock@sha/src_GP_RbtGPFFSpike.cxx.o' -c ../src/GP/RbtGPFFSpike.cxx
In file included from ../include/RbtCavity.h:22,
from ../include/RbtDockingSite.h:23,
from ../include/RbtContext.h:21,
from ../include/GP/RbtGPFFSpike.h:19,
from ../src/GP/RbtGPFFSpike.cxx:13:
../include/RbtRealGrid.h:24:10: fatal error: unsupported/Eigen/CXX11/Tensor: No such file or directory
24 | #include <unsupported/Eigen/CXX11/Tensor>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[5/145] Compiling C++ object 'rxdock@sha/src_GP_RbtGPPopulation.cxx.o'.
FAILED: rxdock@sha/src_GP_RbtGPPopulation.cxx.o
c++ -Irxdock@sha -I. -I.. -I../include -I../include/GP -I/usr/local/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++11 -O3 -fPIC -fopenmp -MD -MQ 'rxdock@sha/src_GP_RbtGPPopulation.cxx.o' -MF 'rxdock@sha/src_GP_RbtGPPopulation.cxx.o.d' -o 'rxdock@sha/src_GP_RbtGPPopulation.cxx.o' -c ../src/GP/RbtGPPopulation.cxx
In file included from ../include/RbtCavity.h:22,
from ../include/RbtDockingSite.h:23,
from ../include/RbtContext.h:21,
from ../include/GP/RbtGPFitnessFunction.h:19,
from ../include/GP/RbtGPFFGold.h:19,
from ../include/GP/RbtGPPopulation.h:20,
from ../src/GP/RbtGPPopulation.cxx:13:
../include/RbtRealGrid.h:24:10: fatal error: unsupported/Eigen/CXX11/Tensor: No such file or directory
24 | #include <unsupported/Eigen/CXX11/Tensor>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[6/145] Compiling C++ object 'rxdock@sha/src_lib_RbtBaseIntraSF.cxx.o'.
FAILED: rxdock@sha/src_lib_RbtBaseIntraSF.cxx.o
c++ -Irxdock@sha -I. -I.. -I../include -I../include/GP -I/usr/local/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++11 -O3 -fPIC -fopenmp -MD -MQ 'rxdock@sha/src_lib_RbtBaseIntraSF.cxx.o' -MF 'rxdock@sha/src_lib_RbtBaseIntraSF.cxx.o.d' -o 'rxdock@sha/src_lib_RbtBaseIntraSF.cxx.o' -c ../src/lib/RbtBaseIntraSF.cxx
In file included from ../include/RbtCavity.h:22,
from ../include/RbtDockingSite.h:23,
from ../include/RbtWorkSpace.h:26,
from ../src/lib/RbtBaseIntraSF.cxx:14:
../include/RbtRealGrid.h:24:10: fatal error: unsupported/Eigen/CXX11/Tensor: No such file or directory
24 | #include <unsupported/Eigen/CXX11/Tensor>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[7/145] Compiling C++ object 'rxdock@sha/src_lib_RbtAlignTransform.cxx.o'.
FAILED: rxdock@sha/src_lib_RbtAlignTransform.cxx.o
c++ -Irxdock@sha -I. -I.. -I../include -I../include/GP -I/usr/local/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++11 -O3 -fPIC -fopenmp -MD -MQ 'rxdock@sha/src_lib_RbtAlignTransform.cxx.o' -MF 'rxdock@sha/src_lib_RbtAlignTransform.cxx.o.d' -o 'rxdock@sha/src_lib_RbtAlignTransform.cxx.o' -c ../src/lib/RbtAlignTransform.cxx
In file included from ../include/RbtCavity.h:22,
from ../include/RbtAlignTransform.h:19,
from ../src/lib/RbtAlignTransform.cxx:13:
../include/RbtRealGrid.h:24:10: fatal error: unsupported/Eigen/CXX11/Tensor: No such file or directory
24 | #include <unsupported/Eigen/CXX11/Tensor>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[8/145] Compiling C++ object 'rxdock@sha/src_lib_RbtBaseBiMolTransform.cxx.o'.
FAILED: rxdock@sha/src_lib_RbtBaseBiMolTransform.cxx.o
c++ -Irxdock@sha -I. -I.. -I../include -I../include/GP -I/usr/local/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++11 -O3 -fPIC -fopenmp -MD -MQ 'rxdock@sha/src_lib_RbtBaseBiMolTransform.cxx.o' -MF 'rxdock@sha/src_lib_RbtBaseBiMolTransform.cxx.o.d' -o 'rxdock@sha/src_lib_RbtBaseBiMolTransform.cxx.o' -c ../src/lib/RbtBaseBiMolTransform.cxx
In file included from ../include/RbtCavity.h:22,
from ../include/RbtDockingSite.h:23,
from ../include/RbtWorkSpace.h:26,
from ../src/lib/RbtBaseBiMolTransform.cxx:14:
../include/RbtRealGrid.h:24:10: fatal error: unsupported/Eigen/CXX11/Tensor: No such file or directory
24 | #include <unsupported/Eigen/CXX11/Tensor>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[9/145] Compiling C++ object 'rxdock@sha/src_lib_RbtAromIdxSF.cxx.o'.
FAILED: rxdock@sha/src_lib_RbtAromIdxSF.cxx.o
c++ -Irxdock@sha -I. -I.. -I../include -I../include/GP -I/usr/local/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++11 -O3 -fPIC -fopenmp -MD -MQ 'rxdock@sha/src_lib_RbtAromIdxSF.cxx.o' -MF 'rxdock@sha/src_lib_RbtAromIdxSF.cxx.o.d' -o 'rxdock@sha/src_lib_RbtAromIdxSF.cxx.o' -c ../src/lib/RbtAromIdxSF.cxx
In file included from ../include/RbtCavity.h:22,
from ../include/RbtDockingSite.h:23,
from ../include/RbtWorkSpace.h:26,
from ../src/lib/RbtAromIdxSF.cxx:14:
../include/RbtRealGrid.h:24:10: fatal error: unsupported/Eigen/CXX11/Tensor: No such file or directory
24 | #include <unsupported/Eigen/CXX11/Tensor>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[10/145] Compiling C++ object 'rxdock@sha/src_GP_RbtGPFFHSP90.cxx.o'.
FAILED: rxdock@sha/src_GP_RbtGPFFHSP90.cxx.o
c++ -Irxdock@sha -I. -I.. -I../include -I../include/GP -I/usr/local/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++11 -O3 -fPIC -fopenmp -MD -MQ 'rxdock@sha/src_GP_RbtGPFFHSP90.cxx.o' -MF 'rxdock@sha/src_GP_RbtGPFFHSP90.cxx.o.d' -o 'rxdock@sha/src_GP_RbtGPFFHSP90.cxx.o' -c ../src/GP/RbtGPFFHSP90.cxx
In file included from ../include/RbtCavity.h:22,
from ../include/RbtDockingSite.h:23,
from ../include/RbtContext.h:21,
from ../include/GP/RbtGPFFHSP90.h:19,
from ../src/GP/RbtGPFFHSP90.cxx:13:
../include/RbtRealGrid.h:24:10: fatal error: unsupported/Eigen/CXX11/Tensor: No such file or directory
24 | #include <unsupported/Eigen/CXX11/Tensor>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[11/145] Compiling C++ object 'rxdock@sha/src_lib_RbtBaseInterSF.cxx.o'.
FAILED: rxdock@sha/src_lib_RbtBaseInterSF.cxx.o
c++ -Irxdock@sha -I. -I.. -I../include -I../include/GP -I/usr/local/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++11 -O3 -fPIC -fopenmp -MD -MQ 'rxdock@sha/src_lib_RbtBaseInterSF.cxx.o' -MF 'rxdock@sha/src_lib_RbtBaseInterSF.cxx.o.d' -o 'rxdock@sha/src_lib_RbtBaseInterSF.cxx.o' -c ../src/lib/RbtBaseInterSF.cxx
In file included from ../include/RbtCavity.h:22,
from ../include/RbtDockingSite.h:23,
from ../include/RbtWorkSpace.h:26,
from ../src/lib/RbtBaseInterSF.cxx:14:
../include/RbtRealGrid.h:24:10: fatal error: unsupported/Eigen/CXX11/Tensor: No such file or directory
24 | #include <unsupported/Eigen/CXX11/Tensor>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[12/145] Compiling C++ object 'rxdock@sha/src_lib_RbtBaseIdxSF.cxx.o'.
FAILED: rxdock@sha/src_lib_RbtBaseIdxSF.cxx.o
c++ -Irxdock@sha -I. -I.. -I../include -I../include/GP -I/usr/local/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++11 -O3 -fPIC -fopenmp -MD -MQ 'rxdock@sha/src_lib_RbtBaseIdxSF.cxx.o' -MF 'rxdock@sha/src_lib_RbtBaseIdxSF.cxx.o.d' -o 'rxdock@sha/src_lib_RbtBaseIdxSF.cxx.o' -c ../src/lib/RbtBaseIdxSF.cxx
In file included from ../include/RbtCavity.h:22,
from ../include/RbtDockingSite.h:23,
from ../include/RbtWorkSpace.h:26,
from ../src/lib/RbtBaseIdxSF.cxx:14:
../include/RbtRealGrid.h:24:10: fatal error: unsupported/Eigen/CXX11/Tensor: No such file or directory
24 | #include <unsupported/Eigen/CXX11/Tensor>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[13/145] Compiling C++ object 'rxdock@sha/src_GP_RbtGPFFGold.cxx.o'.
FAILED: rxdock@sha/src_GP_RbtGPFFGold.cxx.o
c++ -Irxdock@sha -I. -I.. -I../include -I../include/GP -I/usr/local/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++11 -O3 -fPIC -fopenmp -MD -MQ 'rxdock@sha/src_GP_RbtGPFFGold.cxx.o' -MF 'rxdock@sha/src_GP_RbtGPFFGold.cxx.o.d' -o 'rxdock@sha/src_GP_RbtGPFFGold.cxx.o' -c ../src/GP/RbtGPFFGold.cxx
In file included from ../include/RbtCavity.h:22,
from ../include/RbtDockingSite.h:23,
from ../include/RbtContext.h:21,
from ../include/GP/RbtGPFitnessFunction.h:19,
from ../include/GP/RbtGPFFGold.h:19,
from ../src/GP/RbtGPFFGold.cxx:13:
../include/RbtRealGrid.h:24:10: fatal error: unsupported/Eigen/CXX11/Tensor: No such file or directory
24 | #include <unsupported/Eigen/CXX11/Tensor>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[14/145] Compiling C++ object 'rxdock@sha/src_lib_RbtBaseObject.cxx.o'.
FAILED: rxdock@sha/src_lib_RbtBaseObject.cxx.o
c++ -Irxdock@sha -I. -I.. -I../include -I../include/GP -I/usr/local/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++11 -O3 -fPIC -fopenmp -MD -MQ 'rxdock@sha/src_lib_RbtBaseObject.cxx.o' -MF 'rxdock@sha/src_lib_RbtBaseObject.cxx.o.d' -o 'rxdock@sha/src_lib_RbtBaseObject.cxx.o' -c ../src/lib/RbtBaseObject.cxx
In file included from ../include/RbtCavity.h:22,
from ../include/RbtDockingSite.h:23,
from ../include/RbtWorkSpace.h:26,
from ../src/lib/RbtBaseObject.cxx:15:
../include/RbtRealGrid.h:24:10: fatal error: unsupported/Eigen/CXX11/Tensor: No such file or directory
24 | #include <unsupported/Eigen/CXX11/Tensor>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
[15/145] Compiling C++ object 'rxdock@sha/src_lib_RbtBaseFileSource.cxx.o'.
[16/145] Compiling C++ object 'rxdock@sha/src_lib_RbtBaseMolecularFileSink.cxx.o'.
[17/145] Compiling C++ object 'rxdock@sha/src_lib_RbtBaseGrid.cxx.o'.
[18/145] Compiling C++ object 'rxdock@sha/src_lib_RbtBaseMolecularFileSource.cxx.o'.
ninja: build stopped: subcommand failed.Vedran Miletić (fe4ffe4b) at 11 Aug 09:26
Updated RxTx links
Hello,
I'm working with a metalloenzyme that has a catalytic Zinc center. I want to incorporate the Zinc atom vdw parameters into the Tripos52_vdw.prm file, but I don't understand what the K value means. I'm assuming that the R value is the vdw radius of the atom and I was going to use a 1.200 value for the Zinc atom; as the rest of the metals in the file. I'm searching for references to acquire those values because I understand that Zinc has variable coordination. Can you please help me with this issue?
Many thanks,
Islam K. Matar