1. Introduction to Impact

1.1 A Brief History of Impact		A Brief History of Impact
1.2 Major Features		Major Features of Impact
1.3 Hardware Requirements
1.4 Installation		Installing Impact on Your System
1.5 Input Files		Brief discussion of Impact Input Files.
1.6 Structure File Formats		Molecular Structure Formats Supported
1.7 Force Field		Molecular Force Fields Supported
1.8 Web-Based Information Source		Availability of this Document on the Web

1.1 A Brief History of Impact

The current commercial Impact was developed from the academic Impact originally designed in the laboratory of Professor Ronald M. Levy at Rutgers University. The following people have contributed to the development of Impact:

1.1.1 Commercial Versions		Versions developed at Schrodinger
1.1.2 Academic Versions		Versions developed at Rutgers

1.1.1 Commercial Versions

• v1.8 (September 2001). Jay Banks, Yixiang Cao, Wolfgang Damm, Richard Friesner, Thomas Halgren, Emilio Gallicchio, Ronald Levy, Daniel Mainz, and Rob Murphy.

• v1.7 (March 2001). Jay Banks, Yixiang Cao, Richard Friesner, Emilio Gallicchio, Thomas Halgren, Ronald Levy, Daniel Mainz, Rob Murphy, and Ruhong Zhou.

• v1.6 (November 2000). Jay Banks, Michael Beachy, Yixiang Cao, Richard Friesner, Emilio Gallicchio, Ronald Levy, Daniel Mainz, Rob Murphy, and Ruhong Zhou.

• v1.0 (June 1999). Jay Banks, Richard Friesner, Emilio Gallicchio, Avijit Ghosh, Ronald Levy, Rob Murphy, Anders Wallqvist, and Ruhong Zhou.

• v0.95 (Nov 1998). Jay Banks, Richard Friesner, Emilio Gallicchio, Avijit Ghosh, Ronald Levy, Rob Murphy, Anders Wallqvist, and Ruhong Zhou.

• v0.9 (Aug 1998). Jay Banks, Mark Friedrichs, Richard Friesner, Emilio Gallicchio, Avijit Ghosh, Ronald Levy, Rob Murphy, Anders Wallqvist, and Ruhong Zhou.

• v0.8 (May 1998). Jay Banks, Chris Cortis, Shlomit Edinger, Mark Friedrichs, Richard Friesner, Emilio Gallicchio, Avijit Ghosh, Ronald Levy, Rob Murphy, Anders Wallqvist, and Ruhong Zhou.

1.1.2 Academic Versions

• V7.0 (August 1996). Jay Banks, Yanbo Ding, Gabriela Del Buono, Francisco Figueirido, Ronald Levy, and Ruhong Zhou.

• V6.0 (January 1994). Les Clowney, Francisco Figueirido, Ronald Levy, Lynne Reed, Maureen Smith-Brown, Asif Suri and John Westbrook.

• V5.8 (December 10, 1991). Les Clowney, Francisco Figueirido, Douglas Kitchen, Ronald Levy, Maureen Smith, Asif Suri and John Westbrook.

• V5.7 (December 17, 1990). Steve Back, Teresa Head-Gordon, Douglas Kitchen, Dorothy Kominos, Ronald Levy and John Westbrook.

• V5.5 and earlier (June 1990). Steve Back, Donna Bassolino, John Blair, Fumio Hirata, Douglas Kitchen, David Kofke, Dorothy Kominos, Ronald Levy, Asif Suri and John Westbrook.

1.2 Major Features

• Build Protein/DNA/RNA from Residue Sequences
• Energy Minimization
• Molecular Dynamics
• Monte Carlo Methods
• Free-Energy Perturbation
• Fast Multipole Method (FMM)
• Multiple Time-step Algorithm r-RESPA
• S-Walking/J-Walking Methods
• Explicit Solvation Model
• Poisson-Boltzmann Continuum Solvation (PBF)
• Surface Generalized Born Solvation Model (SGB)
• OPLS-AA with Automatic Atomtype Recognition
• Flexible Schemes for Freezing Part of System
• QSite: Mixed-Mode QM/MM Simulations for Reactive Chemistry
• Liaison: Calculating and Predicting Ligand Binding Energies
• Glide: High-Throughput Ligand-Receptor Docking

1.3 Hardware Requirements

Schrödinger, Inc. tests and distributes Impact 1.9 for only SGI IRIX and Intel-x86 compatible Linux-based machines at this time. Ports to other platforms are under development. For current information unsupported platforms, please contact Schrödinger.

1.4 Installation

To install Impact please see the FirstDiscovery Installation Guide. A printed version of this manual and other documentation should come with your CD-ROM. PostScript, PDF, and HTML version for most of the FirstDiscovery manuals should be on the CD-ROM itself.

For those that want to cut to the chase, installation is often as easy as running:

% /bin/sh INSTALL

from the CD-ROM, and following the prompts. But please see the Installation Guide.

After installation, in the directory specified by your $SCHRODINGER environment variable, there should be directory `impact-v1.9'. In that directory, there are four subdirectories it: `bin', `data', `samples' and `tutorial'. The `bin' directory should have the executable binaries and scripts for running all manner of Impact-based jobs. The `data' directory contains the database parameters of OPLS and AMBER force fields; and the `samples' directory contains the example files noted in this manual, while the `tutorial' directory contains files that correspond to the instructional material in the FirstDiscovery Quick Start Guide that walks you through various types of FirstDiscovery calculations.

The single important environment variable each Impact user has to have is $SCHRODINGER. It should be set to your top-level installation directory for Schrödinger products, e.g. /usr/local/bin/schrodinger. If you plan on using some of the utility scripts from a command-line interface, you might like to add the directory $SCHRODINGER/utilities to your PATH enviroment variable, so that the scripts in this directory are accessible by name without the full directory name prepended. If your command-line shell is sh, ksh, or bash, this is done by:

(sh/ksh/bash)% export PATH=${PATH}:$SCHRODINGER/utilities

and if your shell is csh or tcsh, then do:

(csh/tcsh)% setenv PATH ${PATH}:$SCHRODINGER/utilities

To run an Impact example, first make sure that $SCHRODINGER is set to your Schrödinger installation directory. Then cd to one of example directory and type:

% $SCHRODINGER/impact -i input_file -o log_file

This will read from the input_file and write the log file to log_file. If -o is not specified, Impact will set the log file name to be the same as your input file, but with a .log extension in place of .inp.

Note that the log file (stdout) is not the file specified in the top write command in the input file, which is usually more detailed than the log file. Just typing impact with no arguments is equivalent to typing main1m: the program then looks for an input file named `fort.1', and writes to standard output. If an input file is specified but a log file is not, Impact constructs the log file name by appending the suffix .log to the input file name, after first removing the suffix .inp if it is present. Thus

% impact -i myfile

and

% impact -i myfile.inp

will both result in writing a log file called myfile.log.

1.5 Input Files

!! MAININPUT  tutor.inp tutor.inp  Main input file
!! MAINOUTPUT tutor.out tutor.out  Main output file
!! INPUT paramstd paramstd           Energy parameter file
!! INPUT tip4p.con tip4p.con         Energy constraints
!! INPUT tip4p.rst tip4p.rst         Coordinate and velocity restart file
!! DESCRIPTION FILE tutor.des
!! TITLE Tutorial example 

WRITE file tutor.out -
   title TIP4P Water MD *

CREATE
   build solvent name solvent1 type tip4p nmol 216 h2o
QUIT

SETMODEL
   setpotential
      mmechanics 
   quit
   read parm file paramstd noprint
   enrg parm lowcutoff 7.5 upcutoff 9.5 listupdate 10 diel 1.0 nodist
   enrg periodic name solvent1 bx 18.6353 by 18.6353 bz 18.6353
   enrg cons read file tip4p.con
   enrg molcut name solvent1
QUIT

DYNAMICS
  input cntl -
      nstep 1000 delt 0.001 stop rotations -
      constant totalenergy nprnt 50 tol 1.e-7
  read restart coordinates and velocities box real8 -
    formatted file tip4p.rst
  run 
QUIT

END

write file fname title your_favorite_title *
end

After the opening write statement, one specifies a sequence of tasks that Impact should execute. In Impact tasks correspond to a high-level description of the computer experiment. For example, the task create sets up the internal variables describing the molecular structure of the system of interest, while inside of task dynamics one runs a molecular dynamics simulation. Typically it is important that tasks are executed in the correct order, which is usually dictated by common sense (the least common of the senses).(2)

A task by itself does not produce any side effects. For instance, the fragment

create quit

would do exactly nothing. When Impact begins executing a task it sets up a special environment, which is task-dependent. This environment exists until the keyword quit is encountered, closing the task. Within each of these environments different collections of commands (subtasks) are in effect. For instance, within the create task one can execute the subtask build, but it is not defined inside of the task dynamics. Trying to execute build inside of the latter task would lead to an error.

Impact requires that tasks (as well as their matching quit) be declared on a line by themselves. Subtasks, on the other hand, come in several flavors. They must always be the first non-blank word on a line and most often they are followed on the same line by a series of subtask-specific keywords and parameter values. A few, however, have the same formatting requirements as tasks do, and must be ended by the keyword quit.(3)

In general, task and subtask names can be abbreviated by giving the first four characters of the full name. In addition, some special abbreviations are recognized. For example: minimize can be entered as minm; energy can be given as enrg (as illustrated above); ...

Because Impact is written mostly in FORTRAN the implementation puts a limit on the maximum length of a line of 2000 characters. As the lines are scanned lowercase letters are automatically converted to uppercase, unless protected as shown below.(4) The following characters are special:

`"'

To protect a word and preserve the case. For example, if you want to open a file named `/home/me/FooBar', you must write `"/home/me/FooBar"'.

`!'

An exclamation point `!' flags a comment, and anything following it until the end of the line is not read or processed.

`-'

A hyphen at a line's end indicates the command is continued on the next line of the input file. Note that there should be at least one space before the hyphen and that the sum of the lengths of the continued lines must not exceed the limit of 2000 characters.

`$'

String constants are delimited by this character as in `$foo$'.

`''

The quote is used to delimit names of variables used in Impact input files, as in `while 'foo' lt 10'.

`*'

Sometimes portions of command lines are terminated with an asterisk. It is required wherever it appears in the examples. This character is also used as a wild-card in some strings used to access tables (see section 4.4 Table).

The top level of Impact is the task level where the objects of primary interest are described, such as system creation, molecular dynamics or energy minimization. When describing tasks in this documentation, meta-examples are generally used, where the following conventions are followed. The order of the keywords inside a subtask is generally not important though, of course, a keyword cannot be separated from its value when one is required.

keywords

that must be typed exactly as shown will appear in this font;

variables

are meta-keywords, that is, you must replace variable with the appropriate keyword, number, or filename;

[ ]

is used to delimit keywords that are optional; an extra character, `+' or `*', may also be present. [ ]+ means to repeat the contents one or more times and [ ]* to repeat the contents zero or more times.(5) For example

[ foo | bar | baz ]

means that one of the keywords foo or bar or baz may be used in this location. If there are no `|' characters present the body is always optional, and if there is a a `+' immediately following the `]', as in `[ foo ]+', then repeat the contents 1 or more times (here 1 or more occurrences of foo).

nil

stands for the "empty item," that is, no item at all, so that `[ foo | nil ]' is equivalent to `[ foo ]'.

( )

in an example indicates that the contents of the parentheses is repeated as many times as indicated by the following expression. In the following expression the symbols `foo bar baz' are repeated four times.

( foo bar baz ) repeated four times

Using the above rules, the meta-example

You should [ run | debug ] Impact [ when it rains | nil ] is expanded in any of the following statements You should run Impact when it rains You should debug Impact when it rains You should run Impact You should debug Impact

One instance of a meta-example for the minimization task is:

minimize read restart coordinates formatted file fname steepest dx0 value dxm value deltae value run write restart coordinates formatted file fname quit

where value refers to the value to be assigned to the preceding keyword, and fname refers to a file name. (6)

Some keywords are common to many different tasks and subtasks, so they are described here. Note that while only the first four characters of most keywords are significant to Impact, this is subject to change; all keywords should be written as shown.

file

This keyword must be followed by the name of a file. In the meta-examples this is generally shown as fname.(7)

name

This keyword must be followed by the name of a species. In the meta-examples this is generally shown as spec.

resnumber

This keyword must be followed by the number (integer value) of a residue. In the meta-examples this is generally shown as resn. It should be noted that residue numbers supplied in the main input file have the following meanings: positive numbers mean the residue numbering used in the original PDB file; negative numbers mean the reordered Impact residue numbers (i.e., sequential, starting with 1); 0 means all applicable residues.

atname

This keyword must be followed by the name (character string) of an atom. In the meta-examples this is generally shown as atna.

fresidue

lresidue

These keywords should be followed by a number specifying the first and last residues of interest in the primary sequence.

echoon

echooff

These keywords can appear at the task level, or the subtask level of task analysis. They turn on or off the printing of certain output. The default is echoon.

An aid to gauging the correctness of an input file is that, in general, as each command is processed it is deleted from the command line. When processing is finished, a check is made to see that no characters remain. The presence of extraneous characters indicates that the input file was incorrectly formed.

This document frequently refers to input files that may be used as examples. For example, in C.3.3 Electrostatic Potential and Hydration Energy Differences, a system of formaldehyde in water is first created and molecular dynamics is performed and a trajectory file is created. The trajectory is subsequently read, and statistics are gathered on the full dynamics run.

1.6 Structure File Formats

Via the build primary type auto (see section 2.2.1.5 Primary type Auto) and build types (see section 2.2.1.11 Types) commands, Impact can read and write Maestro, MDL SD, and PDB files.

Historically, Impact used PDB file formats for all input structure files, and this is still required for the AMBER86 force field. Other file formats have to be converted into PDB files first before any Impact simulations can be performed in such situations.

The freely available program Babel is a program that converts different file formats, and currently supports input file formats:

Input file type 1. Alchemy 2. AMBER PREP 3. Ball and Stick 4. MSI BGF 5. Biosym .CAR 6. Boogie 7. Cacao Cartesian 8. Cambridge CADPAC 9. CHARMm 10. Chem3D Cartesian 1 11. Chem3D Cartesian 2 12. CSD CSSR 13. CSD FDAT 14. CSD GSTAT 15. Dock PDB 16. Feature 17. Free Form Fractional 18. GAMESS Output 19. Gaussian Z-Matrix 20. Gaussian Output 21. Hyperchem HIN 22. MDL Isis 23. Mac Molecule 24. Macromodel 25. Micro World 26. MM2 Input 27. MM2 Ouput 28. MM3 29. MMADS 30. MDL MOLfile 31. MOLIN 32. Mopac Cartesian 33. Mopac Internal 34. Mopac Output 35. PC Model 36. PDB 37. JAGUAR Input 38. JAGUAR Output 39. Quanta 40. ShelX 41. Spartan 42. Spartan Semi-Empirical 43. Spartan Mol. Mechanics 44. Sybyl Mol 45. Sybyl Mol2 46. Conjure 47. UniChem XYZ 48. XYZ 49. XED 50. M3D

and output file formats:

Output file type 1. DIAGNOTICS 2. Alchemy 3. Ball and Stick 4. BGF 5. Batchmin Command 6. Cacao Cartesian 7. Cacao Internal 8. CAChe MolStruct 9. Chem3D Cartesian 1 10. Chem3D Cartesian 2 11. ChemDraw Conn. Table 12. MSI Quanta CSR 13. Dock Database 14. Wizard 15. Conjure Template 16. CSD CSSR 17. Feature 18. Fenske-Hall ZMatrix 19. Gamess Input 20. Gaussian Cartesian 21. Gaussian Z-matrix 22. Gaussian Z-matrix tmplt 23. Hyperchem HIN 24. Icon 8 25. IDATM 26. Isis 27. Mac Molecule 28. Macromodel 29. Micro World 30. MM2 Input 31. MM2 Ouput 32. MM3 33. MMADS 34. MDL Molfile 35. Mopac Cartesian 36. Mopac Internal 37. PC Model 38. PDB 39. JAGUAR Z-Matrix 40. JAGUAR Cartesian 41. Report 42. Spartan 43. Sybyl Mol 44. Sybyl Mol2 45. MDL Maccs file 46. XED 47. UniChem XYZ 48. XYZ 49. M3D

Before you run babel, you need to setup an environmental variable $BABEL_DIR:

% setenv BABEL_DIR your_babel_directory % export BABEL_DIR= your_babel_directory

The easiest way to run babel is in manual mode:

% babel -m

and follow instructions to select desired input and output file formats. You can also run babel from the command line, as in

% babel -ix myfile.xyz -renum -oai myfile.dat "AM1 MMOK T=30000"

This will create a MOPAC input file with atom 1 from myfile.xyz as atom 1 in myfile.dat. For details of how to run babel, etc, consult the README files under the babel directory. babel also comes with Schrödinger's product Jaguar, and is accessible therein via the jaguar babel command.

1.7 Force Field

1.7.1 AMBER86		The AMBER86 force field
1.7.2 OPLS-AA		The OPLS-AA force field

1.7.1 AMBER86

The AMBER86 force field developed by Kollman and co-workers provides a general description of the intra- and intermolecular interactions. All the atoms are treated explicitly. Although the form of the force field is very general, this force field is chiefly designed to be applied in in the area of molecular biology and thermodynamics of small organic molecules. Given a set of coordinates of the system the total potential energy is calculated from where the intramolecular energy is schematically written as and the non-bonded or intermolecular term is likewise written as The atom-pair distance is denoted and the sum runs over all unique atom pairs. This force field is semi-empirical, i.e. the parameters are derived partly from experimental data (non-bonded terms) and partly from quantum chemical calculations (intramolecular terms). It also contains an empirical model of the dielectric constant modeled as a distant dependent quantity where For molecules containing atoms connected by a distance of more than 3 bond-lengths the atom-atom interaction is given by the V_{inter}-term. However, interactions separated by exactly 3 bond-lengths (1,4-interactions) are scaled by a so called 1,4-scaling factor. A factor of 1/2 is used for both Lennard-Jones and Coulombic interactions. The non-bonded parameters and are constructed by combination rules from a set of van der Waals parameters for the constituent atoms The and are explicitly given for all hydrogen bonded cases.

The AMBER86 force field is currently superseded by the AMBER95 force field developed by the Kollman-group. This new force field omits all explicit hydrogen bond terms. However, Impact does not support AMBER95.

1.7.2 OPLS-AA

The OPLS-AA force field, which was developed by the Jorgensen group, is an effort to develop a parameterization that reproduces liquid state properties of molecules. Again this is a force field that uses experimental data from the liquid state and quantum mechanical calculations for intramolecular bond, angle, and torsion motions to set the constituent parameters. The intramolecular interaction is given as, where written as, The non-bonded interaction is given as a van der Waals terms together with an electrostatic term (R is again the atom-atom distance), Note that in this description the dielectric constant is set to its proper value of 1.0. For molecules containing atoms connected by a distance of more than 3 bond-lengths the atom-atom interaction is given by the -term. The (1,4)-interactions are scaled by a factor of 1/2. The non-bonded parameters and for each atom-pair is constructed from the atomic values by the geometric mean combination rule,

It is also possible to use the partial charges read from a Maestro- or MacroModel-format structure file instead of those provided by OPLS-AA.

1.8 Web-Based Information Source

Schrödinger publishes HTML versions of many product manuals at the website http://www.schrodinger.com/Support/manuals.html. An up-to-date copy of this manual, the FirstDiscovery Reference Manual, along with other FirstDiscovery manuals, are linked there.