Introduction

is the general name for a program that performs as a workbench for computational chemists. In its current version, allows researchers to prepare input for the molecular modeling programs AMBER and SPASMS. Thus, the program replaces the prep, link, edit, and parm programs that used to be distributed with AMBER. It was felt that a replacement was needed that had all such functionality within a single program, that incorporated a simple, consistent user interface, and that would incorporate graphics to allow users to see the systems they were preparing.

The inspiration to write a program to replace the preparation modules of AMBER was first provided by Erik-Robert Evensen while he was at UCSF. Such a program, MainLine, was also written by him. was conceived and written by Christian E. A. F. Schafmeister, working in the laboratory of Peter A. Kollman at the University of California-San Francisco. David A. Rivkin contributed some features and Wilson S. Ross and Vladimir Romanovski have assisted extensively to prepare the program for distribution.

Both and are written in ANSI C. does not support graphics and therefore, it will run in a text window or from a script. is meant to run on any machine that supports X-windows (Version 11 Revision 4 and latter versions). does all of its graphics manipulations in generic X-windows. It does not depend on any system-dependent graphics to do 3D transformations or page-flipping. All of the user interface was written using David E. Smyth's Widget Creation Library (Wcl-1.05). This library is included in the distribution, as is the Xraw 3D widget set by Vladimir Romanovski (modeled on the ATHENA 3D widget set by Kaleb Keithley).

Using , the user can:

Read AMBER PREP input files
Read AMBER PARM format parameter sets
Read and write Object File Format files (OFF)
Read and write PDB files
Construct new residues and molecules using simple commands
Link together residues and create nonbonded complexes of molecules
Place counterions around a molecule
Solvate molecules in arbitrary solvents
Add bond, angle, and torsion restraints to molecules
Modify internal coordinates within a molecule
Generate files that contain topology and parameters for AMBER and SPASMS

In addition, with the user can:

Access commands using a simple point and click interface
Draw new residues and molecules in a graphical environment
View structures graphically
Graphically dock molecules
Modify the properties of atoms, residues, and molecules using a
spreadsheet editor
Input or alter molecular mechanics parameters using a spreadsheet editor.

supports the following input and output file formats:

1. Object File Format (OFF): This is a general file format developed for but applicable to any scientific computing problem. is capable of both reading and writing these files.
2. AMBER PREP input files: The program can read and write these files. Note that when reading, it ignores improper torsions in these files (used to keep things like amino groups planar), instead generating its own impropers from connectivity and whatever force field information is available when AMBER PARM output files are written. When writing PREP files, adds all possible improper torsions, leaving it to the user to decide which are needed. (See Appendix C for a description of improper torsions.)
3. AMBER PARM formatted parameter set files (parm.dat): The formatted parameter set files have been used as an input file for the AMBER program PARM. These files can be read by .
4. AMBER PARM output files: The AMBER PARM output files are coordinate and topology files that are used as input to the programs AMBER and SPASMS. The program can generate these files (prmtop and prmcrd).
5. PDB files: is capable of reading and generating these files.