DOCSLIB.ORG

GMXPBSA 2.0: a GROMACS Tool to Perform MM/PBSA and Computational Alanine Scanning✩

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
GMXPBSA 2.0: a GROMACS Tool to Perform MM/PBSA and Computational Alanine Scanning✩ Computer Physics Communications 185 (2014) 2920–2929 Contents lists available at ScienceDirect Computer Physics Communications journal homepage: www.elsevier.com/locate/cpc GMXPBSA 2.0: A GROMACS tool to perform MM/PBSA and computational alanine scanningI C. Paissoni a, D. Spiliotopoulos a,1, G. Musco a, A. Spitaleri a,b,∗ a Biomolecular NMR Unit, S. Raffaele Scientific Institute, via Olgettina 58, Milan 20132, Italy b Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy article info a b s t r a c t Article history: GMXPBSA 2.0 is a user-friendly suite of Bash/Perl scripts for streamlining MM/PBSA calculations on Received 9 January 2014 structural ensembles derived from GROMACS trajectories, to automatically calculate binding free energies Received in revised form for protein–protein or ligand–protein complexes. GMXPBSA 2.0 is flexible and can easily be customized 19 May 2014 to specific needs. Additionally, it performs computational alanine scanning (CAS) to study the effects Accepted 17 June 2014 of ligand and/or receptor alanine mutations on the free energy of binding. Calculations require only Available online 2 July 2014 for protein–protein or protein–ligand MD simulations. GMXPBSA 2.0 performs different comparative analysis, including a posteriori generation of alanine mutants of the wild-type complex, calculation of Keywords: Molecular dynamics simulation the binding free energy values of the mutant complexes and comparison of the results with the wild-type Binding free energy system. Moreover, it compares the binding free energy of different complexes trajectories, allowing the Virtual screening study the effects of non-alanine mutations, post-translational modifications or unnatural amino acids on GROMACS the binding free energy of the system under investigation. Finally, it can calculate and rank relative affinity Computational alanine scanning to the same receptor utilizing MD simulations of proteins in complex with different ligands. In order to MM/PBSA dissect the different MM/PBSA energy contributions, including molecular mechanic (MM), electrostatic contribution to solvation (PB) and nonpolar contribution to solvation (SA), the tool combines two freely available programs: the MD simulations software GROMACS and the Poisson–Boltzmann equation solver APBS. All the calculations can be performed in single or distributed automatic fashion on a cluster facility in order to increase the calculation by dividing frames across the available processors. The program is freely available under the GPL license. Program summary Program title: GMXPBSA 2.0 Catalogue identifier: AETQ_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AETQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 185 937 No. of bytes in distributed program, including test data, etc.: 7 074 217 Distribution format: tar.gz Programming language: Bash, Perl. Computer: Any computer. Operating system: Linux, Unix OS. RAM: ∼2 GB I This paper and its associated computer program are available via the Computer Physics Communication homepage on ScienceDirect (http://www.sciencedirect.com/ science/journal/00104655). ∗ Corresponding author at: Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy. Tel.: +39 3485188790. E-mail address: [email protected] (A. Spitaleri). 1 Present address: Computational Structural Biology Biochemisches Institut Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland. http://dx.doi.org/10.1016/j.cpc.2014.06.019 0010-4655/' 2014 Elsevier B.V. All rights reserved. C. Paissoni et al. / Computer Physics Communications 185 (2014) 2920–2929 2921 Classification: 3. External routines: APBS (http://www.Poissonboltzmann.org/apbs/) and GROMACS installations (http:// www.gromacs.org). Optionally LaTeX. Nature of problem: Calculates the Molecular Mechanics (MM) data (Lennard-Jones and Coulomb terms) and the solvation energy terms (polar and nonpolar terms respectively) from an ensemble of structures derived from GROMACS molecular dynamics simulation trajectory. These calculations are performed for each single component of the simulated complex, including protein and ligand. In order to cancel out artefacts an identical grid setup for each component, including complex, protein and ligand, is required. Performs statistical analysis on the extracted data and comparison with wild-type complex in case of either computational alanine scanning or calculations on a set of simulations. Evaluates possible outliers in the frames extracted from the simulations during the binding free energy calculations. Solution method: The tool combines the freely available programs GROMACS and APBS to: 1. extract frames from a single or multiple complex molecular dynamics (MD) simulation, allowing comparison between multiple trajectories; 2. split the complex frames in the single components including complex, protein and ligand; 3. calculate the Lennard-Jones and Coulomb energy values (MM terms); 4. calculate the polar solvation energy values using the implicit solvation Poisson–Boltzmann model (PB); 5. calculate the nonpolar solvation energy value based on the solvent accessible surface area (SASA); 6. combine all the calculated terms into the final binding free energy value; 7. repeat the same procedure from point 1 to 6 for each simulation in case of computational alanine scanning (CAS) or simultaneous comparison of different MDs. Restrictions: Input format files compatible with GROMACS engine 4.5 and later versions. Availability of the force field or of the topology files. Running time: On a single core, Lennard-Jones, Coulomb and nonpolar solvation terms calculations require a few min- utes. The time required for polar solvation terms calculations depends on the system size. ' 2014 Elsevier B.V. All rights reserved. 1. Introduction where Eint indicates bond, angle, and torsional angle energies, and Ecoul and ELJ denote the intramolecular electrostatic and Lennard- MM/PBSA is a versatile method to calculate the binding free en- Jones energies, respectively. ergies of a protein–ligand complex [1]. It incorporates the effects The solvation term Gsolv in Eq. (4) is split into polar Gpolar and of thermal averaging with a force field/continuum solvent model nonpolar contributions, Gnonpolar: to post-process a series of representative snapshots from MD trajectories. MM/PBSA has been successfully applied to compute Gsolv D Gpolar C Gnonpolar (4) the binding free energy of numerous protein–ligand interactions GMXPBSA 2.0 calculates G and G with Adaptive Pois- [2–5]. The method expresses the free energy of binding as the dif- polar nonpolar son–Boltzmann Solver (APBS) program [7]. ference between the free energy of the complex and the free energy The polar contribution G refers to the energy required to of the receptor plus the ligand (end-state method). This difference polar transfer the solute from a continuum medium with a low dielectric is averaged over a number of trajectory snapshots [6]. Of note, the constant (" D 1) to a continuum medium with the dielectric con- MM/PBSA approach allows for a rapid estimation of the variation stant of water (" D 80). G is calculated using the non-linearized in the free energy of binding, with the caveat that generally it does polar or linearized Poisson–Boltzmann equation. The nonpolar contribu- not reproduce the absolute binding free energy values. Neverthe- tion G is considered proportional to the solvent accessible less, it usually exhibits good correlations with experiments, thus nonpolar surface area (SASA): representing a fair compromise between efficiency and efficacy for the calculation and comparison of binding free energy variations. Gnonpolar D γ SASA C β (5) The theory underlying MM/PBSA approach has been described pre- − −2 − viously [6]. Briefly, the binding free energy of a protein molecule to where γ D 0:0227 kJ mol 1Å and β D 0 kJ mol 1 [8]. The di- a ligand molecule in solution is defined as: electric boundary is defined using a probe of radius 1.4 Å. Binding free energy calculations based on the MM/PBSA ap- ∆Gbinding D Gcomplex − .Gprotein C Gligand/: (1) proach can be performed either according to the three trajecto- A MD simulation is performed to generate a thermodynamically ries method (TTM) or to the single trajectory method (STM). The weighted ensemble of structures. The free energy term is calcu- TTM requires three separate MD simulations on the three system lated as an average over the considered structures: components including the complex, the free ligand and the free re- ceptor. This is a computationally demanding approach and prone hGi D hEMMi C hGsolvi − T hSMMi: (2) to structural noise [3,5]. Conversely, the STM requires a single tra- The energetic term E is defined as: MM jectory run for the complex, whereby both the protein and ligand EMM D Eint C Ecoul C ELJ (3) structures are extracted directly from the complex structure [3], 2922 C. Paissoni et al. / Computer Physics Communications 185 (2014) 2920–2929 Fig. 1. Workflow diagram for GMXPBSA 2.0. Diagram describing the general GMXPBSA 2.0 workflow scheme. GMXPBSA 2.0 combines the GROMACS and APBS programs in order to use the frames extracted from the molecular dynamics simulations and to calculate the binding free energy. thus zeroing out the Eint term. In this
Load more

Recommended publications
  • Open Babel Documentation Release 2.3.1
    Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) December 05, 2011 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Filtering molecules from a multimolecule file .............................. 22 3.8 Substructure and similarity searching .................................. 25 3.9 Sorting molecules ............................................ 25 3.10 Remove duplicate molecules ....................................... 25 3.11 Aliases for chemical groups ....................................... 26 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options .................................................
    [Show full text]
  • Structural Insight Into Pichia Pastoris Fatty Acid Synthase Joseph S
    www.nature.com/scientificreports OPEN Structural insight into Pichia pastoris fatty acid synthase Joseph S. Snowden, Jehad Alzahrani, Lee Sherry, Martin Stacey, David J. Rowlands, Neil A. Ranson* & Nicola J. Stonehouse* Type I fatty acid synthases (FASs) are critical metabolic enzymes which are common targets for bioengineering in the production of biofuels and other products. Serendipitously, we identifed FAS as a contaminant in a cryoEM dataset of virus-like particles (VLPs) purifed from P. pastoris, an important model organism and common expression system used in protein production. From these data, we determined the structure of P. pastoris FAS to 3.1 Å resolution. While the overall organisation of the complex was typical of type I FASs, we identifed several diferences in both structural and enzymatic domains through comparison with the prototypical yeast FAS from S. cerevisiae. Using focussed classifcation, we were also able to resolve and model the mobile acyl-carrier protein (ACP) domain, which is key for function. Ultimately, the structure reported here will be a useful resource for further eforts to engineer yeast FAS for synthesis of alternate products. Fatty acid synthases (FASs) are critical metabolic enzymes for the endogenous biosynthesis of fatty acids in a diverse range of organisms. Trough iterative cycles of chain elongation, FASs catalyse the synthesis of long-chain fatty acids that can produce raw materials for membrane bilayer synthesis, lipid anchors of peripheral membrane proteins, metabolic energy stores, or precursors for various fatty acid-derived signalling compounds1. In addition to their key physiological importance, microbial FAS systems are also a common target of metabolic engineering approaches, usually with the aim of generating short chain fatty acids for an expanded repertoire of fatty acid- derived chemicals, including chemicals with key industrial signifcance such as α-olefns2–6.
    [Show full text]
  • Francisella Novicida Cas9 Interrogates Genomic DNA with Very High Specificity and Can Be Used for Mammalian Genome Editing
    Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing Sundaram Acharyaa,b,1, Arpit Mishraa,1,2, Deepanjan Paula,1, Asgar Hussain Ansaria,b, Mohd. Azhara,b, Manoj Kumara,b, Riya Rauthana,b, Namrata Sharmaa, Meghali Aicha,b, Dipanjali Sinhaa,b, Saumya Sharmaa,b, Shivani Jaina, Arjun Raya,3, Suman Jainc, Sivaprakash Ramalingama,b, Souvik Maitia,b,d, and Debojyoti Chakrabortya,b,4 aGenomics and Molecular Medicine Unit, Council of Scientific and Industrial Research—Institute of Genomics & Integrative Biology, New Delhi, 110025, India; bAcademy of Scientific & Innovative Research, Ghaziabad, 201002, India; cKamala Hospital and Research Centre, Thalassemia and Sickle Cell Society, Rajendra Nagar, Hyderabad, 500052, India; and dInstitute of Genomics and Integrative Biology (IGIB)-National Chemical Laboratory (NCL) Joint Center, Council of Scientific and Industrial Research—National Chemical Laboratory, Pune, 411008, India Edited by K. VijayRaghavan, Tata Institute of Fundamental Research, Bangalore, India, and approved September 6, 2019 (received for review October 27, 2018) Genome editing using the CRISPR/Cas9 system has been used to has shown variable levels of off targeting due to tolerance of make precise heritable changes in the DNA of organisms. Although mismatches predominantly in the “nonseed” region in the sgRNA, the widely used Streptococcus pyogenes Cas9 (SpCas9) and its wherever these are encountered in the genome (20). To what engineered variants have been efficiently harnessed for numerous extent FnCas9 mediates this high specificity of target interrogation gene-editing applications across different platforms, concerns re- is not known and whether these properties can be harnessed for main regarding their putative off-targeting at multiple loci across highly specific genome editing at a given DNA loci has not been the genome.
    [Show full text]
  • Hands-On Tutorials of Autodock 4 and Autodock Vina
    Hands-on tutorials of AutoDock 4 and AutoDock Vina Pei-Ying Chu (朱珮瑩) Supervisor: Jung-Hsin Lin (林榮信) Research Center for Applied Sciences, Academia Sinica 2018 Frontiers in Computational Drug Design, Academia Sinica, March 16-20, 2018 AutoDock http://autodock.scripps.edu AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock 4 is free and is available under the GNU General Public License. 2 AutoDock Vina http://vina.scripps.edu/ Because the scoring functions used by AutoDock 4 and AutoDock Vina are different and inexact, on any given problem, either program may provide a better result. AutoDock Vina is available under the Apache license, allowing commercial and 3 non-commercial use and redistribution. http://autodock.scripps.edu/downloads These programs were installed on VM. 4 http://mgltools.scripps.edu/ AutoDockTools (ADT) is developed to help set up the docking. ADT is included in MGLTools packages. 5 In general, each docking (AutoDock 4 and/or AutoDock Vina) requires: 1. structure of the receptor (protein), in pdbqt format 2. structure of the ligand (small molecule, drug, etc.) in pdbqt format 3. docking and grid parameters (search space) PDBQT format is very similar to PDB format but it includes partial charges ('Q') and AutoDock 4 (AD4) atom types ('T'). • Preparing the ligand involves ensuring that its atoms are assigned the correct AutoDock4 atom types, adding Gasteiger charges if necessary, merging non-polar hydrogens, detecting aromatic carbons if any, and setting up the 'torsion tree'.
    [Show full text]
  • Modeling and Simulation of Single Stranded RNA Viruses
    MODELING AND SIMULATION OF SINGLE STRANDED RNA VIRUSES A Dissertation Presented to The Academic Faculty by Mustafa Burak Boz In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the School of Chemistry and Biochemistry Georgia Institute of Technology August 2012 MODELING AND SIMULATION OF SINGLE STRANDED RNA VIRUSES Approved by: Dr. Stephen C. Harvey, Advisor Dr. Roger Wartell School of Biology School of Biology Georgia Institute of Technology Georgia Institute of Technology Dr. Rigoberto Hernandez Dr. Loren Willams School of Chemistry & Biochemistry School of Chemistry & Biochemistry Georgia Institute of Technology Georgia Institute of Technology Dr. Adegboyega Oyelere School of Chemistry & Biochemistry Georgia Institute of Technology Date Approved: June 18, 2012 Dedicated to my parents. ACKNOWLEDGEMENTS I would like to thank my family for their incredible support and patience. I would not have been here without them. I especially would like to give my gratitude to my father who has been the most visionary person in my life leading me to towards my goals and dreams. I would also like to thank to Dr. Harvey for being my wise and sophisticated advisor. I am also grateful to the all Harvey Lab members I have known during my Ph. D years, (Batsal Devkota, Anton Petrov, Robert K.Z. Tan, Geoff Rollins, Amanda McCook, Andrew Douglas Huang, Kanika Arora, Mimmin Pan, Thanawadee (Bee) Preeprem, John Jared Gossett, Kazi Shefaet Rahman) for their valuable discussions and supports. TABLE OF CONTENTS Page ACKNOWLEDGEMENTS
    [Show full text]
  • Atpase Via Molecular Dynamic Simulations
    TEMPORAL AND STERIC ANALYSIS OF IONIC PERMEATION AND BINDING IN NA+,K+-ATPASE VIA MOLECULAR DYNAMIC SIMULATIONS A dissertation presented to the faculty of the Russ College of Engineering and Technology of Ohio University In partial fulfillment of the requirements for the degree Doctor of Philosophy James E. Fonseca June 2008 2 c 2008 James E. Fonseca All rights reserved 3 This dissertation entitled TEMPORAL AND STERIC ANALYSIS OF IONIC PERMEATION AND BINDING IN NA+,K+-ATPASE VIA MOLECULAR DYNAMIC SIMULATIONS by JAMES E. FONSECA has been approved for the Department of Electrical Engineering and Computer Science and the Russ College of Engineering and Technology of Ohio University by Savas Kaya Associate Professor of Electrical Engineering and Computer Science Dennis Irwin Dean, Russ College of Engineering and Technology 4 Abstract Fonseca, James, Ph.D., June 2008, Electrical Engineering Temporal and Steric Analysis of Ionic Permeation and Binding in Na+,K+-ATPase via Molecular Dynamic Simulations (206 pp.) Director of Dissertation: Savas Kaya Interdisciplinary research has become a mature approach for the development of novel, integrated solutions for many complex problems in basic science and applied technology. The convergence of biology and nanotechnology is particularly promising from an engineering perspective. This dissertation will use computer simulations to investigate the structure-function of the P-type ATPases, a class of vital biological transmembrane proteins. A detailed understanding of protein function at the atomic level and associated time scale is not only important for biomedical research but also vital for the design and development of engineering applications, such as self- assembling molecular devices.
    [Show full text]
  • Molecular Dynamics Study of Voltage-Gated Sodium/Potassium Channels Daniel Bauer and Prof
    Project Manager Molecular Dynamics Study of Daniel Bauer voltage-gated Sodium/Potassium Principal Investigator channels Prof. Dr. Kay Hamacher Project Term Daniel Bauer and Prof. Dr. Kay Hamacher 2018 - 2019 Clusters Lichtenberg Cluster Darmstadt Software GROMACS Additional Software PLUMED, APBS, MODELLER Institute Computational Biology and Simulation University Technische Universität Darmstadt Figure 1: The sodium/potassium channel HCN1 embedded into a membrane bilayer. HCN1 is shown as green cartoon, membrane as balls and sticks and ions as purple/green spheres. The blue surface represents water. Introduction Ion channels play a fundamental key role in all living organisms and are crucial for the signal transduction of neurons in higher animals. In human, the hyperpolarization-activated cyclicnucleotide-gated (HCN) sodium/potassium channels of the HCN family are crucial for various biological processes. In the neural and cardiovascular system, they are responsible for the pacemaker current (also known as funny current If), which is characterized by a slow and rhythmic mixed sodium and potassium influx into cells. Mutations in the genes of the HCN family have been linked to various diseases, including rhythmias, epilepsies and neuropathic pain.[1] Even though discovered several decades ago, only little is known about why HCN channels act so different compares to their relatives (potassium selective channels). However, the recently printed 04. Oct 2021 - 21:58 https://www.hkhlr.de/projects/1689 page 1 of 3 Molecular Dynamics Study of voltage-gated Sodium/Potassium channels Daniel Bauer and Prof. Dr. Kay Hamacher revealed 3D structure of one member of this family — HCN1 — allows us to use computational simulation techniques to investigate some of the key aspects of these channels: HCN channelsare only weakly potassium selective and they activate at hyperpolarizing voltages.[2] Methods We use MD simulations of protein/membrane systems to simulate potassium channels embedded into membrane systems.
    [Show full text]
  • Open Source Molecular Modeling
    Accepted Manuscript Title: Open Source Molecular Modeling Author: Somayeh Pirhadi Jocelyn Sunseri David Ryan Koes PII: S1093-3263(16)30118-8 DOI: http://dx.doi.org/doi:10.1016/j.jmgm.2016.07.008 Reference: JMG 6730 To appear in: Journal of Molecular Graphics and Modelling Received date: 4-5-2016 Accepted date: 25-7-2016 Please cite this article as: Somayeh Pirhadi, Jocelyn Sunseri, David Ryan Koes, Open Source Molecular Modeling, <![CDATA[Journal of Molecular Graphics and Modelling]]> (2016), http://dx.doi.org/10.1016/j.jmgm.2016.07.008 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Open Source Molecular Modeling Somayeh Pirhadia, Jocelyn Sunseria, David Ryan Koesa,∗ aDepartment of Computational and Systems Biology, University of Pittsburgh Abstract The success of molecular modeling and computational chemistry efforts are, by definition, de- pendent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. 1. Introduction What is Open Source? Free and open source software (FOSS) is software that is both considered \free software," as defined by the Free Software Foundation (http://fsf.org) and \open source," as defined by the Open Source Initiative (http://opensource.org).
    [Show full text]
  • Pymol– Tutorial
    Pymol– Tutorial Exercise 1: Introduction “File –> Open” 3OG7 Save your session by doing “File –> Save Session As...” (don’t forget to save your work regularly by “File –> Save Session” PyMol can open more tHan one molecule at a time, or separate complex PDB files into individual components. Each opened or loaded molecule is given a name witHin tHe “Names Panel” (rigHt part of the window). THe first name is always “all.” Clicking on the name itself will undisplay the corresponding molecule(s) (temporarily invisible). Clicking again on the name will display tHe molecule. The ASHLC menu is abbreviated for Action, Show, Hide, Label and Color. For example, for a better overview “S”“SHow as”“cartoon”. This Hides everytHing and sHows tHe protein’s backbone representation. Go to tHe following menu cascade: Setting > Cartoon > Cylindrical Helices Select tHis option again to remove its effect and do the following: Setting > Cartoon > Fancy Helices PyMol is optimized for a 3-button mouse: Rotation around the X or Y axis: (left) click and drag Rotation around the Z axis: (left) click on the top left or rigHt corner Translate (move sideways) X or Y: click middle button and drag Zoom (move along Z axis): click rigHt button and drag up or down Now start to “experiment” witH your mouse. BIOCHEMISTRY 660 / 712 – FALL 2006 J.Y. SGRO 6) Final image(s) If you still see the selection dots over the ligand from the previous section simply click anywhere on the white background to unselect. Alternatively click on the “Hide-Sele” button at the top right hand side of the “external GUI.” BIOCHEMISTRY 660 / 712 – FALL 2006 J.Y.
    [Show full text]
  • Pymol Handout PSB-CIBB
    PyMOL Handout PSB-CIBB Babu A. Manjasetty PhD Cyril Dian PhD MariaRosa Quintero Bernabeu PhD 1 1 Introduction to the software PyMOL is a molecular viewer, render tool, and 3D molecular editor intended for visu- alization of 3D chemical structures including atomic resolution X-ray crystal structures of: proteins, nucleic acids (DNA, RNA, and tRNA), and carbohydrates, as well as small molecule structures of drug leads, inhibitors, metabolites, sugars, nucleoside phosphates, and other ligands including inorganic salts and solvent molecules. PyMOL is a USER- SPONSORED molecular visualization system on an OPEN-SOURCE foundation. 1.1 Visualization To visualize a 3D structure the file has to be in the right format. The supported formats are: .pml PyMOL command script to be run on startup .py, .pym, .pyc Python program to be run on startup .pdb Protein Data Bank format file to be loaded on startup .mmod Macromodel format to be loaded on startup .mol MDL MOL file to be loaded on startup .sdf MDL SD file to be parsed and loaded on startup .xplor X-PLOR Map file (ASCII) to be loaded on startup .ccp4 CCP4 map file (BINARY) to be loaded on startup .cc1, .cc2 ChemDraw 3D cartesian coordinate file .pkl Pickled ChemPy Model (class \chempy.model.Indexe") .r3d Raster3D file .cex CEX file (Metaphorics) .top AMBER topology file .crd AMBER coordinate file .rst AMBER restart file .trj AMBER trajectory .pse PyMOL session file .phi Delphi/Grasp Electrostatic Potential Map Once your structure is loaded, you can modify it. The simplest actions are: • close-up: zoom-in and out • surface/map: The surface representation of a protein, in PyMol, shows the "Con- nolly" surface or the surface that would be traced out by the surfaces of waters in contact with the protein at all possible positions.
    [Show full text]
  • APBS 0.5.1 User Guide 10/30/07 10:10 AM
    APBS 0.5.1 User Guide 10/30/07 10:10 AM APBS 0.5.1 User Guide Adaptive Poisson-Boltzmann Solver Nathan A Baker Washington University in St. Louis Department of Biochemistry and Molecular Biophysics Center for Computational Biology Copyright © 2002, 2003, 2004, 2005, 2006, 2007 Washington University in St. Louis This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111- 1307 USA Linking APBS statically or dynamically with other modules is making a combined work based on APBS. Thus, the terms and conditions of the GNU General Public License cover the whole combination. SPECIAL GPL EXCEPTION: In addition, as a special exception, the copyright holders of APBS give you permission to combine the APBS program with free software programs and libraries that are released under the GNU LGPL or with code included in releases of ISIM, Ion Simulator Interface, PMV, PyMOL SMOL, VMD, and Vision. Such combined software may be linked with APBS and redistributed together in original or modified form as mere aggregation without requirement that the entire work be under the scope of the GNU General Public License.
    [Show full text]
  • Open Babel Documentation
    Open Babel Documentation Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) Mar 26, 2021 Contents 1 Introduction 3 1.1 Goals of the Open Babel project.....................................3 1.2 Frequently Asked Questions.......................................4 1.3 Thanks..................................................7 2 Install Open Babel 11 2.1 Install a binary package......................................... 11 2.2 Compiling Open Babel.......................................... 11 3 obabel - Convert, Filter and Manipulate Chemical Data 19 3.1 Synopsis................................................. 19 3.2 Options.................................................. 19 3.3 Examples................................................. 22 3.4 Format Options.............................................. 24 3.5 Append property values to the title.................................... 24 3.6 Generating conformers for structures.................................. 24 3.7 Filtering molecules from a multimolecule file.............................. 25 3.8 Substructure and similarity searching.................................. 28 3.9 Sorting molecules............................................ 28 3.10 Remove duplicate molecules....................................... 28 3.11 Aliases for chemical groups....................................... 29 3.12 Forcefield energy and minimization................................... 30 3.13 Aligning molecules or substructures..................................
    [Show full text]