Now Antechamber supports jaguar cartesian input and output, divcon cartesian input and output
Now Antechamber supports both CM1 and CM2 - needs the divcon 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
Move an atom (specified by -a1) or the geometric center of the molecule to the cartesian coordinate orgin.
Translate the molecule; the X-vector, Y-vector and Z-vector are specified by -vx, -vy, -vz, respectively.
Rotate the molecule by an amount (in degrees, specified by -d) along the axis defined by two atoms (specified by -a1 and -a2).
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)).
Do a least-squares fit, wth the reference molecule being read in with "-r" flag.
Two empirical QM programs are supported: mopac (mopac.sh) and divcon (divcon). Here are the rules:
mopac.sh takes "mopac.in" and output mopac.out; divcon takes "divcon.in" and output "divcon.out"
If only $AMBERHOME is defined, divcon is applied
If only $ACHOME is defined, mopac.sh is applied
If both $AMBERHOME and $ACHOME are defined, divcon is applied in default, however if "-df" is set to 0, mopac.sh is used
If neigher $AMBERHOME nor $ACHOME are defined, mopac.sh 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.
Several bugs were detected and removed.
A new example, nad, was added.