4.1 The Generate Command - Construct a Segment of the PSF

4.1.1 Syntax

     GENErate [segid] [NBXMod int] [rtf-type] [CYCLic]
     
              [[NO]ANGLes] [NOTORSions      ] [[NO]DONOrs] [[NO]ACCEptors]
                           [TORSions {ALL}]
                           [         {ONE}]
     
                  { PROT }
                  { HPRO }
                  { ALLH }
     rtf-type ::= { DNA  }
                  { A94N }
                  { A94P }
                  { AM94 }

4.1.2 Function

Using the sequence of residues specified in the last READ SEQUENCE command and the information stored in the residue topology file, this command generates the next segment in the PSF. Each segment contains a list of all the bonds, angles, dihedral angles, and improper torsions needed to calculate the energy. It also assigns charges to all the atoms, sets up the nonbonded exclusions list, and specifies hydrogen bond donors and acceptors. If a special type of segment has been specified in the READ SEQUENCE command or by the rtf-type option, modifications for structural features not contained in the residue topology file, for example terminal group modifications and proline modifications, are made automatically. The CYCLIC option controls whether a cyclic structure is built. Cyclic structures are made by omitting any terminal residues, and wrapping references to atoms beyond each end of the segment back to the other end.

The processing of terminal groups varies depending on the rtf-type setting. If a CONGEN topology file is read; rtf-type equals PROT, HPRO, ALLH, or DNA; then extra residues, like NTER and CTER, are added to the sequence. This has the undesirable side-effect of adding extra residues into your sequence, and confusing the residue numbering.

If the AMBER 94 potential is used, a different scheme is used. Here, the topology file, AMBER94RTF, contains special terminal residues, which have different atoms and charges. The GENERATE command will translate the terminal residues to the names in the topology file, generate the segment, and then translate the names back. The following example table illustrates the naming conventions used for alanine.

ALA

Regular alanine.

NALA

N terminal alanine.

CALA

C terminal alanine.

DALA

D alanine.

MALA

N terminal D alanine.

BALA

C terminal D alanine.

The A94P keyword specifies that an AMBER 94 protein sequence is to be generated, and the A94N keyword specifies a nucleic acid sequence is to be generated. As a special case, leucinol (LEOH) is handled correctly.

The GENERATE command is capable of automatically generating some of the information needed to compute the energies from other sources within the PSF. In the case of the AMBER potential, CONGEN sets these options on by default. In addition, the value of these switches is saved in the PSF (in the NICTOT array), so that they can be used by the SPLICE command, see Splice Command. The automatic generation options have the following interpretations:

ANGLES

NOANGLES

Specifies that bond angles are to be generated from the bond list. All bonds joined by a common atom will be added to the angle list, and all duplicates removed. The keyword, NOANGLES, turns this option off.

TORSIONS

NOTORSIONS

Specifies that torsion angles are to be generated from the bond list. This process begins by CONGEN looping over all bonds in the system. It will then examine all atoms bound to the two atoms in the selected bond, and If the keyword ONE is specified, the program will add a torsion for the first pair of bound atoms which are both non-hydrogen. If no pair of heavy atoms can be found, then the program will select the first pair of bound atoms. If the keyword ALL is specified, then all sets of four atoms connected by three bonds in tandem will be added as torsions. Note that this code detects three membered rings and will ignore them. In addition, you must specify either ONE or ALL if you specify TORSIONS. The keyword, NOTORSIONS, turns off this option.

DONORS

ACCEPTORS

Specifies that hydrogen bond donors and acceptors be added automatically. This depends critically on the atom type specifications in the residue topology file, see RTF Mass Command. The keywords, NODONORS and NOACCEPTORS, turn off these options, respectively.

NBXMOD

The NBXMOD option controls the automatic generation of non-bonded exclusions, see Nbxmod, for more details.

The actual generation process proceeds in four phases. First, all the atoms specified by the residues are added to the PSF. Next, all the terms are added, and all linkage references can be correctly handled, see Linkage Atom Naming. Next, the automatic generation operations are performed. Finally, the patches are performed.