FANTOM

Version 4.2 (July 1998)

User Manual

 

Numan Oezguen, Kizhake Soman, Robert Fraczkiewicz, Christian Mumenthaler, Berthold von Freyberg, Thomas Schaumann and Werner Braun

Sealy Center for Structural Biology

Department of Human Biological Chemistry & Genetics

University of Texas Medical Branch

Galveston., TX 77555, U.S.A.

Institut fur Molekularbiologie und Biophysik

Eidgenossische Technische Hochschule

CH - 8093 Zurich, Switzerland

 

 

 

 

This project is supported by the National Science Foundation (grants DBI-9632326 and DBI-9714937), the Department of Energy of the United States of America (grant DE-FG03-96ER62267) and the Sealy & Smith Foundation.

Table of Contents

1. Introduction

2. Installation *

3. Input Files *

3.1 Amino acid residue library and nomenclature *

3.2 Atomic solvation parameters *

3.3 Amino acid sequence and dihedral angles *

3.4 Distance constraints *

3.5 Dihedral angle constraints *

3.6 Conformational sampling restrictions *

3.7 Symmetry library *

3.8 FANTOM file *

4. Running FANTOM *

4.1 Interactive input *

4.2 General commands *

4.3 Constraints *

4.4 Minimization *

4.5 Monte Carlo simulation *

4.6 Homology modeling *

4.7 Low energy paths between two structures *

5. Output Files *

5.1 Amino acid sequence and dihedral angles *

5.2 Atomic coordinates *

5.3 Atomic surface areas *

5.4 Violations of constraints *

5.5 Monte Carlo simulation overview *

5.6 Set of improved conformations *

5.7 Ranking of conformations *

5.8 Grid search *

5.9 FANTOM file *

6. Examples Illustrating the Use of FANTOM *

6.1 Minimization of enkephalin *

6.1.1 Minimization in vacuo *

6.1.2 Minimization including protein-solvent interactions *

6.2 Constrained minimization of tendamistat in vacuo *

6.3 Monte Carlo simulation of enkephalin *

6.4 Loop sampling of a neurotoxin *

6.5 Regularization of the PDB structure of ubiquitin *

6.6 Homology modeling of the vee virus coat protein *

6.6.1 Raw model generation by EXDIS *

6.6.2 Structure regularization by FANTOM *

6.6.3 Restrained energy minimization by FANTOM *

6.6.4 Unrestrained energy minimization by FANTOM *

6.7 Low-energy pathway between two structures of ubiquitin *

7. Error Messages *

8. References *

9. Index of Commands *