Command List by Function

 

Table of Contents

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
 

Input/Output 
Command  Arguments Notes
close  Filename  Close the file (Filename) opened with 'output'
dump  {forcefield terms}  Output forcefield terms (e.g. dump atom bond angle)
echo  on/off Turn on/off message printing 
output Filename  Open file (Filename) for writing 
read Filename  Read an AMMP file (Filename)
 
 
Energy Minimization 
Command  Arguments Notes
bfgs Niter Toler  BFGS quasi-newton optimizer with (Niter) number of iterations and a tolerance equal to (Toler)
cndgel  Niter Nreset Toler Poliak-Ribeire conjugate gradient algorithm. Perform (Niter) iterations with (Nreset) iterations between resets to steepest descent direction and a tolerance equal to (Toler).
genetic ?? 
grasp ?? 
gsdg  Niter I J Gauss-Siedal Distance Geometry on atoms (I-J) with (Niter) iterations. See GSDG page for more information.
polytope I J Niter Vstart Vfinal  Perform polytope simplex optimization on atoms (I-J). Use (Niter) iterations with a starting variance (Vstart) and target variance (Vfinal).
rigid I J Niter Vstart Vfinal  Perform quartenion rigid-body optimization. Same arguments as polytope 
rigid ?? 
steep Niter Toler  Steepest decent optimizer using (Niter) iterations and tolerance equal to (Toler).
tgroup id i1 i2 i3 i4  See torsion search page 
tmap i1 i2 i3 i4 j1 j2 j3 j4 n1 n2 See torsion search page 
tmin ii j k l nstep  See torsion search page 
tset ii j k l angle  See torsion search page 
trunc ?? 
trust ?? 
 

Molecular Dynamics 
Command  Arguments Notes
v_maxwell T [Vx Vy Vz Set the velocity distribution to be Maxwell-Boltzmann with a temperature equal to (T). Use optional systematic drift velocity of (Vx,Vy,Vz
v_rescale Rescale the velocities to a new temperature (T
hpac  ?? See Molecular Dynamics page 
pac  ?? See Molecular Dynamics page 
pacpac  ?? See Molecular Dynamics page 
ptpac  ?? See Molecular Dynamics page 
tpac  ?? See Molecular Dynamics page 
normal  Damp Calculates the normal modes. If Damp is greater than 0 display them. Normal uses a finite difference approach to the force matrix and can be rather slow with more than 50 or so atoms.
 

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   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 AOutput the value of the variable (A).
nzinactiveI JInactivate 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 ZTether 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.  
serialA Rname AnameSet 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).