4.3 Input commands

 

There are the commands to perform the AMMP input.

 

 

ABC   (UINT)Atom1   (UINT)Atom2   (UINT)Atom3   (FLOAT)Theta   (FLOAT)ThetaZero   (FLOAT)Dr   (FLOAT)Dk1   (FLOAT)Dk2
 

Define the angle - bond correlation.

Parameters:
Atom1    Atom serials for angle selection.
Atom2  
Atom3  
Theta   Angle value in degree.
ThetaZero   Angle constant.
Dr   Distance.
Dk1   Distance constant 1.
Dk2   Distance constant 2.

Return message:
None.

 

Example:
None.

 

See also:
ANGLE, USE.

ANGLE   (UINT)Atom1   (UINT)Atom2   (UINT)Atom3   (FLOAT)Kf   (FLOAT)Theta
 

Define an angle.

Parameters:
Atom1    Atom serials for angle selection.
Atom2  
Atom3  
Kf   Force constant.
Theta   Angle value in degree.

Return message:
None.

 

Example:
ANGLE   11   10   33   48.622711   109.470001;

 

See also:
ATOM, BOND, HYBRID, MOMPAR, TORSION, USE.

ATOM   (FLOAT)X   (FLOAT)Y   (FLOAT)Z   (UINT)Serial   (CHAR)Name   (FLOAT)Charge   (FLOAT)A   (FLOAT)B   (UFLOAT)Mass
 

Add a new atom.

Parameters:
X   Atom Cartesian coordinates.
Y  
Z  
Serial    Atom serial number.
Name   Atom name in residue.atom format. It must be in lower case.
Charge   Atomic charge.
A   Non-bond attractive and repulsive terms.
B  
Mass   Atom mass.

Return message:
None.

 

Example:
ATOM   -5.186443   1.313206   -0.020967   1   unk.c   -0.048661   26.171595   1056.904541   12.010700;

 

See also:
ANGLE, ATOM, BOND, HYBRID, MOMPAR, TORSION, USE.

AV5   (UINT)Atom1   (UINT)Atom2   (UINT)Atom3   (UINT)Atom4   (FLOAT)Kf   (FLOAT)Offset
 

Define a tetrahedral "volume" or centroid. This term forces tetrahedral atoms to be tetrahedral and introduces some mixing between angles and bonds.

Parameters:
Atom1    Atom serials defining the tetrahedral volume.
Atom2  
Atom3  
Atom4  
Kf   Force constant.
Offset   Angle offset in degree.

Return message:
None.

 

Example:
None.

 

See also:
USE.

BOND   (UINT)Atom1   (UINT)Atom2   (FLOAT)Length   (FLOAT)Kf  (FLOAT)BondOrder
 

Define a bond.

Parameters:
Atom1    Atom serials for bond selection.
Atom2  
Length   Bond length in Å.
Kf   Force constant.
BondOrder  

This is an optional field not used in the AMMP calculations, but useful to assign the correct bond order when the AMMP file is loaded. It's a floating point number in the 0 to 3 range where 0 is undefined bond order, 1.0 single, 1.5 partial double, 2.0 double and 3.0 triple. Bond orders less than 1.5 are considered single (e.g. 1.25) and bond orders greater than 1.5 but less or equal than 2.0 are considered double.

Return message:
None.

 

Example:
BOND   10   11   1.489000   346.172668;

 

See also:
ANGLE, ATOM, HYBRID, MOMPAR, TORSION, USE.

EXPAND   (UINT)Osn   (UINT)N   (FLOAT)A   (FLOAT)R   ...
 

Expand an orbital. The A and R parameters can be repeated up to six times.

Parameters:
Osn    Orbital serial number.
N   Number of terms.
A   Weight for Gaussians.
R   Radius for Gaussians.

Return message:
None.

 

Example:
None.

 

See also:
DSCF, ORBIT.

HYBRID   (UINT)Atom1   (UINT)Atom2   (UINT)Atom3   (UINT)Atom4   (FLOAT)Kf   (FLOAT)Theta
 

Define a hybrid (improper) angle.

Parameters:
Atom1    Atom serials for hybrid angle selection.
Atom2  
Atom3  
Atom4  
Kf   Force constant.
Theta   Angle value in degree.

Return message:
None.

 

Example:
HYBRID   7   9   10   8   150.000000   0.000000;

 

See also:
ANGLE, ATOM, BOND, MOMPAR, TORSION, USE.

INIT4D   (FLOAT)HowMuch
 

Initialize the 4D non-bonded energy for embedding as implemented in CHARMM, generating pseudo-random w coordinates.

Parameters:
HowMuch    It's the scale value to generate the pseudo-random w coordinates (default 1.0).

Return message:
None.

 

Example:
INIT4D   1.0;

 

See also:
USE.

MOMPAR   (UINT)Atom   (FLOAT)Chi   (FLOAT)Jaa
 

Define the electronegativity and the self coulomb terms. It's useful to place this command after the corresponding atom record allowing the AMMP burst mode in the atom serial search.

Parameters:
Atom    Atom serial.
Chi   Elecronegativity.
Jaa   Self coulomb term.

Return message:
None.

 

Example:
MOMPAR   9   8.241000   13.364000;

 

See also:
ANGLE, ATOM, BOND, MOM, MOMADD, HYBRID, TORSION, USE.

MORSE   (UINT)Atom1   (UINT)Atom2   (FLOAT)Kf   (FLOAT)Order
 

Define a Morse bond. The Morse potential can be computed by the following equation:

 

V = Kf *(1 - exp ( - Order * (RAtom1, Atom2 - REAtom1, Atom2))2

 

where V is the potential, Kf is the bond force constant, RAtom1, Atom2 is the bond length,  REAtom1, Atom2 is the bond length at equilibrium, Order control the width of the potential.

Parameters:
Atom1    Atom serials for bond selection.
Atom2  
Kf   Force constant.
Order   Control the width of the potential.

Return message:
None.

 

Example:
None.

 

See also:
BOND, USE.

NOEGEN   (FLOAT)Di   (FLOAT)Dh
 

Set the noels to the current geometry.

Parameters:
Dl    Low distance threshold in Å.
Dh   High distance threshold in Å.

Return message:
None.

 

Example:
None.

 

See also:
NOEL, USE.

NOEL   (UINT)Atom1   (UINT)Atom2   (FLOAT)D   (FLOAT)Dl   (FLOAT)Dh   (FLOAT)Kl   (FLOAT)Kh
 

Noe distance restraint.

Parameters:
Atom1    Atom serials.
Atom2  
D   Base distance in Å.
Dl   Low distance threshold in Å.
Dh   High distance threshold in Å.
Kl   Force constant for low distance threshold.
Kh   Force constant for high distance threshold.

When the noel is switched on (see USE), the potential (V) is calculated starting from the distance (R) between Atom1 and Atom2:


if R < Dl   V = (R - (D - Dl))^2 * Kl
if R > Dh   V = (R - (D + Dh))^2 * Kh

 

Return message:
None.

 

Example:
None.

 

See also:
NOEGEN, STEP, SWARM, USE.

ORBIT   (CHAR)Type   (UINT)Atom1   [(UINT)Atom2   (UINT)Atom3   (UINT)Atom4   (UINT)Atom5]   (UINT)Osn   [(FLOAT)Along   (FLOAT)X   (FLOAT)Y   (FLOAT)Z]   (INT)Spin   (INT)Pair
 

Define an orbital for SCF calculation.

Parameters:
Type    Orbital type. It could be: 1, 1o, 2, 3, 4s, 4p, m.
  
Orbital Description
1 1 center 1s.
1o 1 center 1s arbitrary origin.
2 2 center (on a bond) 1s.
3 3 center (on an angle diagonal) 1s.
4s 4 center asymmetric (one sided) on a plane normal (e.g. nitrogen).
4p 4 center symmetric (one sided) on a plane normal.
m Multicentred on atoms (e.g. Pi-greco orbital for benzene).

The command can assume different arguments on the basis of the orbital type:

 

ORBIT   1   (UINT)Atom1   (UINT)Osn   (INT)Spin   (INT)Pair

ORBIT   1o   (UINT)Atom1   (UINT)Osn   (FLOAT)Along   (FLOAT)X   (FLOAT)Y   (FLOAT)Z   (INT)Spin   (INT)Pair

ORBIT   2   (UINT)Atom1   (UINT)Atom2   (UINT)Osn   (FLOAT)Along   (INT)Spin   (INT)Pair
ORBIT   3   (UINT)Atom1   (UINT)Atom2   (UINT)Atom3   (UINT)Osn   (FLOAT)Along   (FLOAT)X   (INT)Spin   (INT)Pair

ORBIT   4s   (UINT)Atom1   (UINT)Atom2   (UINT)Atom3   (UINT)Atom4   (UINT)Osn   (FLOAT)Along   (INT)Spin   (INT)Pair

ORBIT   4p   (UINT)Atom1   (UINT)Atom2   (UINT)Atom3   (UINT)Atom4   (UINT)Osn   (FLOAT)Along   (INT)Spin   (INT)Pair

ORBIT   m   (UINT)Atom1   (UINT)Atom2   (UINT)Atom3   (UINT)Atom4   (UINT)Atom5   (UINT)Atom6   (UINT)Osn   (INT)Spin   (INT)Pair
Atom1   Atom serial numbers.
Atom2  
Atom3  
Atom4  
Atom5  
Atom6  
Osn   Orbital serial number.
Along   Direction.
X   Origin Cartesian coordinates or X only (along2) for 3 orbital type.
Y  
Z  
Spin   Spin.
Pair   It can be 1 (singlet) or 2 (doublet, default).

Return message:
None.

 

Example:
None.

 

See also:

DSCF, EXPAND.

READ   (CHAR)FileName
 

Read an AMMP command file.

Parameters:
FileName    File name to load.

Return message:
None.

 

Example:
READ   "MyFile.amp";

 

See also:
None.

RESET
Reset all clearing all variables and the atoms. The AMMP environment is reverted to the empty status.

 

Parameters:
None.

 

Return message:
None.

 

Example:
RESET;

 

See also:
None.

RESTRAIN   (UNIT)Atom1   (UINT)Atom2   (UFLOAT)Length   (UFLOAT)Kf
 

Define a restraint between two atoms.

Parameters:
Atom1   Atom serial numbers.
Atom2  
Length   Distance length in Å
Kf   Force constant.

Return message:
None.

 

Example:
RESTRAIN   12   15   3.0   280.0;

 

See also:
NOEL, TETHER.

STEP   (UNIT)Atom1   (UINT)Atom2   (UFLOAT)D1   (UFLOAT)D2   (UFLOAT)D3   (UFLOAT)Kf1   (UFLOAT)Kf2   (UFLOAT)Kf3
 

Define a step distance (3 point noel).

Parameters:
Atom1   Atom serial numbers.
Atom2  
D1   Distances in Å.
D2  
D3  
Kf1   Force constants.
Kf2  
Kf3  

Return message:
None.

 

Example:
None.

 

See also:
NOEL, SWARM, USE.

SWARM   (UFLOAT)Kf   (UNIT)Atom1   [...   (UINT)Atom8]
 

Add a distance restrain to the mean distance.

Parameters:
Kf1   Force constant.
Atom1   Atom serial numbers.
...  
Atom8  

Return message:
None.

 

Example:
None.

 

See also:
NOEL, STEP, USE.

TABLE   (UINT)TableID   (UINT)N
 

Create an empty sorted table for the table driven bond potential. It's an alternative to the use of the standard bond potential.  The table contains N sorted bond lengths (R, from the lowest to the highest value) and the correspondent N potential values (V, see TABLEENT to add them). To evaluate the Vb bond potential between the i, j atoms, the Rij bond length is calculated and it's compared with the bond lengths stored in the table:Each bond must be defined by the TBOND command that allow to specify the TableID to get the potential values

Parameters:
TableID    Table identification number.
N   Number of table bond lengths (max. 200).

Return message:
None.

 

Example:
TABLE   1   12;

 

See also:
TABLEENT, TBOND.

TABLENT   (UINT)TableID   (UINT)ElemNum   (FLOAT)R   (FLOAT)V
 

Add a new element to the table.

Parameters:
TableID    Table identification number.
ElemNum   Element table number.
R   Distance bond length in Å.
V   Potential value.

Return message:
None.

 

Example:
None.

 

See also:
TABLE, TBOND.

TAILOR   (CHAR)KeyWord   (UINT)Atom1   [(FLOAT)Q   FLOAT)A   (FLOAT)B]   or   [(UINT)Atom2]
 

Set, exclude, include the atoms from the non-bonded list.

Parameters:
KeyWord    It could be: qab to set the non-bond parameter, exclude to exclude an atom range in the non-bond calculation and include to include an atom range in the non-bond calculation. 
Atom1   Atom serial number. Using the exclude and include keywords, it's the first atom in the selection.
Atom2   Atom serial number of the last atom in selection. Available with exclude and include keywords only.
Q   Atomic charge (qab only).
A   Attractive and repulsive non-bond terms (qab only).
B  

Return message:
None.

 

Example:
TAILOR   exclude   1   48;

TAILOR   qab   -0.244565   18.213057   631.409485;

 

See also:
ATOM.

TBOND   (UINT)Atom1   (UINT)Atom2   (UINT)TableID   (FLOAT)Scale
 

Define a bond which potential will be evaluated using the table method.

Parameters:
Atom1    Atom serials for bond selection.
Atom2  
TableID   Table identification number.
Scale   Potential scale factor.

Return message:
None.

 

Example:
TBOND   10   12   1   1.0;

 

See also:
TABLE, TABLEENT, USE.

TETHER   (UINT)Serial   (FLOAT)Kf   FLOAT)X   (FLOAT)Y   (FLOAT)Z
 

Tether an atom to a position.

Parameters:
Serial    Atom serial number. It could be All, tethering all atoms.
Kf   Force constant.
X   Reference position. These arguments are valid only if the serial number is specified.
Y  
Z  

Return message:
None.

 

Example:
TETHER   10   5.0   1.0   -2.0   1.0;
TETHER   all   5.0;

 

See also:
ATOM, USE.

TORSION   (UINT)Atom1   (UINT)Atom2   (UINT)Atom3   (UINT)Atom4   (FLOAT)Kf   (UINT)Mult   (FLOAT)Offset
 

Define a torsion angle.

Parameters:
Atom1    Atom serials for torsion angle selection.
Atom2  
Atom3  
Atom4  
Kf   Force constant.
Mult   Multiplicity.
Offset   Angle value in degree.

Return message:
None.

 

Example:
TORSION   4   5   19   17   1.317616   3   180.000000;

 

See also:
ANGLE, ATOM, BOND, HYBRID, MOMPAR, USE.

TTARGET   (UINT)Atom1   (UINT)Atom2   (UINT)Atom3   (UINT)Atom4   (FLOAT)Angle   (FLOAT)Kf  
 

Define a torsion angle restrain.

Parameters:
Atom1    Atom serials for torsion angle selection.
Atom2  
Atom3  
Atom4  
Angle   Angle value in degree.
Kf   Force constant.

Return message:
None.

 

Example:
None.

 

See also:
TORSION.

VELOCITY   (UINT)Serial   (FLOAT)Vx   (FLOAT)Vy   (FLOAT)Vz
 

Set the velocity to the specified atom.

Parameters:
Serial    Atom serial number.
Vx   X, Y, Z velocity components.
Vy  
Vz  

Return message:
None.

 

Example:
VELOCITY   12   0.0   0.0   0.0;

 

See also:
DOUBLETIME, HPAC, PACPAC, PAC, PPAC, PTPAC, RICHARD, TPAC, V_MAXWELL, V_RESCALE, VERLET.