Molecular Templates

Molecular templates define molecular geometry for preammp. These are named with the same three letter code which appears in the pdb file for the given residue. The file for alanine is shown here:

10

name ala.n type np charge -0.463

name ala.hn type hd charge 0.252

name ala.ca type c3 charge 0.035

name ala.ha type h charge 0.048

name ala.c type c2 charge 0.616

name ala.o type o2 charge -0.504

name ala.cb type c3 charge -0.092

name ala.hb1 type h charge 0.036

name ala.hb2 type h charge 0.036

name ala.hb3 type h charge 0.036

9

ala.n ala.hn 1

ala.n ala.ca 1

ala.ca ala.c 1

ala.ca ala.cb 1

ala.ca ala.ha 1

ala.c ala.o 1.75

ala.cb ala.hb1 1

ala.cb ala.hb2 1

ala.cb ala.hb3 1

0

2

ala.n ala.cb ala.c ala.ca 4 .494427

ala.n ala.cb ala.c ala.ha 4 1.606971

0

Note that the names are given by residue.atom. This "dot notation" is AMMP's way of keeping track of atom names. AMMP will run without it, but will have difficulty referring to atoms by name. There are no special angles, two special hybrids, and no special torsions.

Fractional bond orders are allowed. In this case using C=O with 1.75 and C-N with 1.25 (see peplink.amp) gives the best agreement with experimental lengths.

Chiral centers are expressed as "hybrid" terms. The easiest way to generate these is to first general an a-chiral molecule; use a hybrid term with zero force constant; and then have AMMP calculate the height with analyze. You then only have to set the sign of the height term.

It is possible to overide almost every default in preammp. Atomic parameters and special molecular geometries can be specified in the template file

For the atoms: the name and type fields are required. The use of additional keyword-value pairs allows for optional changes. The most often used pair is (charge,the_charge) which is used to specify atomic paritial charges. (mass, the_mass) sets the atomic mass. (a,a_value), (b,b_value) or (sigma,radius),(e,vdw_energy) can be used to specify the Van der Waals parameters. The order of the keywords is optional.

Special bond, angle, hybrid and torsion parameters can be set. In these the parameters are treated as strings which allows the use of symbolic replacement. For bonds the format is bond atom1 atom2 radius force_constant. The keyword bond is required because bonds are normally defined as atom.res atom.res bond_order. Angles are defined as atom1 atom2 atom3 angle force constant. Hybrids (pyramid height terms) are defined as atom1 atom2 atom3 atom4 height force constant. Torsions are defined as atom1 atom2 atom3 atom4 force_constant period offset.