Kino-geometric sampling (KGS) source

KGS is an engine that generates conformational perturbations in biomolecules (protein, RNA, or ligands alike) by maintaining user-specified non-local constraints. Specifically, collisions are avoided while hydrogen-bonds and disulphide bonds are maintained. A set of applications are built on this engine:

• kgs_explore: Generating conformational ensemble from a seed structure
• kgs_rigidity: Rigidity analysis of structure file
• kgs_hierarchy: Hierarchical kinematic flexibility analysis of structure file
• kgs_transition: Directed sampling from initial structure to target structure
• kgs_relative_transition: Driving conformations

Dependencies

KGS depends as a minimum on the GNU Scientific Library (GSL) only. GSL is available through most standard package managers. For Mac, download homebrew and run brew install gsl.

If the Intel MKL libraries can be found on the system then faster and automatically parallelized SVD computations will be enabled as well.

Compiling

To compile KGS from source go to a terminal and type

git clone https://github.com/ExcitedStates/KGS.git
mkdir KGS/build
cd KGS/build
cmake -DCMAKE_BUILD_TYPE=Release ../src
make -j

After modifying files in src simply type make in the build-dir to recompile. To use Intels compiler (v17.0.3 or later) replace the third step with

CXX=icpc cmake -DCMAKE_BUILD_TYPE=Release <repo path>/source

To compile with debugging symbols and optimizations disabled, open a terminal and type

mkdir debug
cd debug
cmake -DCMAKE_BUILD_TYPE=Debug <repo path>/source
make

This allows debuggers and analysers like gdb, lldb, or valgrind to give meaningful source-code info.

Compiling on Stanfords Sherlock cluster

Sherlock has an old (4.4) GCC compiler and no MKL libraries by default. To compile on Sherlock start an sdev session and from an empty directory type

module load gcc 
module load intel
CXX=`which g++` cmake <repo path>/src
make -j 16

Compiling on SSRLs unix systems at SLAC (including sdc's)

This system has an old (4.4) GCC compiler by default so the newer version 5 should be enabled before running cmake. This is not necessary when subsequently calling make.

scl enable devtoolset-4 bash
cmake <repo path>/src
make -j 16

On sdc04, there is no need to call

scl enable devtoolset-4 bash

Just change to a bash shell:

bash
. /home/sw/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64
cmake <repo path>/src
make -j 16

cmake complains it cannot find gsl, even though it is installed

Make sure the executable

gsl-config

which is part of gsl, is in your path

Usage

Before running, its recommended to put the executables and kgs_prepare.py script somewhere pointed to by the PATH environment variable. A number of options that affect e.g. motion-planning and collision detection can be passed, but a minimum working example is as follows

wget https://files.rcsb.org/download/2ERL.pdb
kgs_prepare.py 2ERL.pdb
kgs_explore --initial 2ERL.kgs.pdb

This should create an output directory and put 10 generated conformations in it (the default number of samples to generate). The prepared .kgs.pdb file has the same coordinates as the original, but atom-ids have been renumbered, and REMARK records indicating hydrogen-bonds have been added.