Forcefield Terms
Command |
Arguments |
Notes |
angle |
I J K Kf Theta |
Define angle (Theta, in degrees) with
atoms (I-K) with force constant (Kf) |
bond |
I J Length Kf |
Define bond (Length, in Angstroms) between
atoms (I-J) with force constant (Kf) |
hybrid |
I J K L Kf Theta |
Define hybrid (Theta, in degrees) with atoms (I-L)
with force constant (Kf) |
momadd |
I J |
Define atoms (I-J) for MOM calculations |
mom |
Q Niter |
Perform MOM charge calculations with a total charge (Q)
and number of iterations (Niter) |
noel |
I J R_mean Delta_low Delta_hi |
Define noel term |
restrain |
I J Length Kf |
Define restraint (Length, in Angstroms)
between atoms (I-J) with force constant (Kf) |
torsion |
I J K L Kf modulus location_of_max |
Define Torsion term |
Mathematical Commands
Command |
Arguments |
Notes |
add |
A B |
Variable (A) is set to (A
+ B) |
div |
A B |
Variable (A) is set to (A
/ B) |
fix |
A |
Variable (A) is rounded down to an integer |
max |
A B |
Variable (A) is set to the maximum of
(A) or (B) |
min |
A B |
Variable (A) is set to the minimum of
(A) or (B) |
mov |
A B |
Variable (A) is set to (B) |
mul |
A B |
Variable (A) is set to (A
* B) |
randf |
A |
Variable (A) is set to a pseudo-random
number |
setf |
A Value |
Define floating point number (A) and set
equal to (Value) |
seti |
A Value |
Define integer number (A)and set equal
to (Value) |
sqrt |
A B |
Variable (A) is set to the square root
of (A) |
sub |
A B |
Variable (A) is set to (A
- B) |
Miscellaneous Commands
Command |
Arguments |
Notes |
active/inactive | I J |
Activate/Inactivate atoms ( I-J ).
Active atoms move while inactive atoms don't. |
analyze | I J | Output the
complete non-bonded and electrostatic energies for atoms ( I-J ).
Useful for determining the interaction energy of a protein/substrate complex. |
nop | A | Output the value
of the variable (A). |
nzinactive | I J | Inactivate all atoms
from ( I-J ) which are not located at the origin (0,0,0). |
tailor | exclude/include I J |
exclude/include atoms ( I-J)
from the non-bonded list. |
tether | Serial Kf X Y Z | Tether an atom
( Serial is the atom serial number) to a position
(X,Y,Z) with a force constant equal to (Kf).
|
use | {forcefield terms} |
Define terms in the potential energy function. All commands in
the Forcefield table above are valid. The
argument none will clear the list. |
serial | A Rname Aname | Set the variable
(A) equal to the serial number given by the atom name
(Aname) of residue (Rname) |
label: | | Define an endpoint for loop and jump commands.
Note that a colon must directly follow (i.e. no spaces) the label command. |
loopf | label: F0 Fmax Df | Define
an floating point loop. Iterate from (F0) to
(Fmax) by the increment (Df). The
(label) defines the end of the loop. |
loopi | label: I0 Imax Di | Define
an integer loop. Iterate from (I0) to
(Imax) by the increment (Di). The
(label) defines the end of the loop. |
je | A B label: | If (A)
is equal to (B) then jump to (label). |
jg | A B label: | If (A)
is greater than (B) then jump to (label). |
jl | A B label: | If (A)
is less than (B) then jump to (label). |