Transcript TinkerTutorial - The Fritz Haber Center for Molecular dynamics

Tutorial
Moshe Goldstein
Fritz Haber Research Center, Hebrew U.
February 13, 2012
Tutorial Plan
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What is TINKER?
Basic Principles of TINKER Operation
What can be done with TINKER?
mgTINKER - my version of TINKER
What can be done with mgTINKER?
What cannot be done with TINKER/mgTINKER?
Using other packages for/with TINKER
Some practice with TINKER and mgTINKER
What is TINKER?
TINKER is a Molecular Mechanics package
developed at Prof. Jay W. Ponder’s Lab, in
the Department of Chemistry at
Washington University, in Saint Louis,
Missouri, USA.
What is TINKER?
• TINKER is a set of relatively independent
programs written in Fortran.
• Until version 5, it was written in (sequential)
Fortran 77.
• The latest version 6, written in Fortran 95,
supports OpenMP parallelism.
Basic Principles of Operation
Molecule Representation
XYZ Cartesian Coordinates
file includes connectivity and
force field-related data
SEQ file that
includes the amino
acids sequence of
a peptide or
protein
PRM file includes force
field parameterization
data
INT Internal Coordinates
file includes Z-Matrix and
force field-related data
Basic Principles of Operation
Cartesian Coordinates Representation
Basic Principles of Operation
Internal Coordinates Representation
Basic Principles of Operation
Peptide Sequence Files
Basic Principles of Operation
Affecting Calculations with a Key Files
Basic Principles of Operation
Allowing Continuation of MD with DYN Files
Basic Principles of Operation
Kinds of Programs
Output
Input
molecule
PROGRAM
molecule
molecule(s)
PROGRAM
Calculated
value(s)
molecule(s)
PROGRAM
molecule(s)
File and/or
cmd params
Translator/
Constructor
File
What can be done
with TINKER?
What can be done
with TINKER?
mgTINKER
my version of TINKER
• mgTINKER is a system of relatively independent
Python scripts that integrate together one or
more TINKER programs.
• TINKER programs are used as basic “black”
boxes, as basic components in order to
accomplish more complex computational tasks.
• The code of several TINKER programs has been
changed, and/or combined in order to execute
new innovating operators/functions.
mgTINKER
my version of TINKER
Tinker 3.9
Tinker 4.0
mgTinker
Tinker 4.1
Mostly
Written in
Python
Tinker 5.1
Tinker 6.0
Written in
Fortran77
Written in
Fortran95 +
OpenMP
What can be done
with mgTINKER?
• DEEPSAM, an evolutionary protein
structure prediction algorithm that
integrates together the advantages of the
Diffusion Equation Method, Simulated
Annealing, L-BFGS and Evolutionary
Programming. It was written in Python,
and uses existing TINKER programs and
also re-written/adapted versions of them.
What can be done
with mgTINKER?
• Several utilities has been written in order
to calculate energies and superposition of
series of structures calculated by
DEEPSAM, and also by minimizations and
simulations like MD, MC, SA, DEM, etc.
What cannot be done
with TINKER/mgTINKER?
• One of the most important disadvantages
of TINKER is that it does not support nonstandard (engineered) amino acids.
• It is possible to add such a capability, but it
requires (a) a lot work in development of
additional force field parameters, and (b)
a lot of programming work – the Fortran
code needs to be expanded to deal with
this.
What cannot be done
with TINKER/mgTINKER?
• TINKER supports calculations with implicit
solvent models like GBSA, with explicit
solvent boxes, in the gas phase, etc., it
supports calculations on clusters of water
and other kinds of molecules, but it does
not support Docking calculations.
• I am not sure if TINKER supports
calculations on complexes of different biomolecules. I need to check this point.
Using other packages
for/with TINKER
• There exists an API between GAMESS
and TINKER that allows QMMM
calculations (I have not tried it yet).
TINKER programs work as Molecular
Mechanics subroutines of GAMESS.
• There exists a program called Packmol
that allows to build an explicit solvent box
and put a bio-molecule inside it,
generating an file processable by TINKER.
• …
Some Practice with TINKER and
mgTINKER
Tutorial
THE END
Moshe Goldstein
Fritz Haber Research Center, Hebrew U.
February 13, 2012