Posted on Nov 10th, 2005

  • Molecular formats
    Now Antechamber supports jaguar cartesian input and output, divcon cartesian input and output

  • Charge methods
    Now Antechamber supports both CM1 and CM2 - needs the divcon program

  • New program
    We have added a new program, translate.c to the Antechamber package. Translate.c performs translation or rotation or least-squared fitting on a file in either pdb, ac or mol2 format. There are five "command" modes, which are
    1. center
      Move an atom (specified by -a1) or the geometric center of the molecule to the cartesian coordinate orgin.
    2. translate
      Translate the molecule; the X-vector, Y-vector and Z-vector are specified by -vx, -vy, -vz, respectively.
    3. rotate1
      Rotate the molecule by an amount (in degrees, specified by -d) along the axis defined by two atoms (specified by -a1 and -a2).
    4. rotate2
      Rotate the molecule by an amount (in degrees, specified by -d) along the axis defined by two points (specified by ((-x1, -y1, -z1) and (-x2, -y2, -z2)).
    5. match
      Do a least-squares fit, wth the reference molecule being read in with "-r" flag.

  • QM program
    Two empirical QM programs are supported: mopac ( and divcon (divcon). Here are the rules:
    1. takes "" and output mopac.out; divcon takes "" and output "divcon.out"
    2. If only $AMBERHOME is defined, divcon is applied
    3. If only $ACHOME is defined, is applied
    4. If both $AMBERHOME and $ACHOME are defined, divcon is applied in default, however if "-df" is set to 0, is used
    5. If neigher $AMBERHOME nor $ACHOME are defined, in the work directory is used.
  • Other executable programs and parameter files
    For other executable programs, such as atomtype, bondtype, am1bcc etc and parameter files, those in $ACHOME have higher priority to be used that those in $AMBERHOME.
  • Molecular rings in Antechamber
    RING *ring is allocated memory dynamically. Now Antechamber can handle molecules, such as bucky ball properly.
  • Message in Antechamber
    Three kinds of message are produced by the Antechamber programs: the information message, the warning message and the error message. One should pay attention to the warning and error message.
  • Bug fixes
    Several bugs were detected and removed.
  • Examples
    A new example, nad, was added.