The molecular topology information must be first generated for the structure - this contains the information about molecular connectivity. This information is then be used in the next step to generate starting (extended conformation) coordinates. The molecular topology is generated from the sequence (not coordinates). This is done with the CNS task file generate_seq.inp.
cns_solve < generate_seq.inp > generate_seq.out [1.5 seconds]
Note that this structure contains 2 separate chains, thus 2 sequence files are made. This will result in a molecular topology with 2 unconnected chains, in CNS there is no way to specify a break in a chain purely based on the sequence. The 2 sequence files have this format:
MET VAL LYS GLN ILE GLU SER LYS THR ALA PHE GLN GLU ALA LEU ASP ALA ALA GLY ASP LYS LEU VAL VAL VAL ASP PHE SER ALA THR TRP CYS GLY PRO ALA LYS MET ILE LYS PRO PHE PHE HIS SER LEU SER GLU LYS TYR SER ASN VAL ILE PHE LEU GLU VAL ASP VAL ASP ASP ALA GLN ASP VAL ALA SER GLU ALA GLU VAL LYS ALA THR PRO THR PHE GLN PHE PHE LYS LYS GLY GLN LYS VAL GLY GLU PHE SER GLY ALA ASN LYS GLU LYS LEU GLU ALA THR ILE ASN GLU LEU VAL
and
PRO ALA THR LEU LYS ILE CYS SER TRP ASN VAL ASP GLY
The two chains are input as 2 different sequence files and given different segment identifiers (for ease of analysis later on). Also, the numbering for the second chain is begun at 106:
{* protein sequence file *}
{===>} prot_sequence_infile_1="trx_a.seq";
{* segid *}
{===>} prot_segid_1="A";
{* start residue numbering at *}
{===>} renumber_1=1;
{* protein sequence file *}
{===>} prot_sequence_infile_2="trx_b.seq";
{* segid *}
{===>} prot_segid_2="B";
{* start residue numbering at *}
{===>} renumber_2=106;
It is also important to include any disulphide bonds at this stage - as they require the addition of bond information to the molecular topology. Here there is a bond between the 2 chains (residue 32 to residue 112):
{=========================== disulphide bonds ==============================}
{* Select pairs of cysteine residues that form disulphide bonds *}
{* First 2 entries are the segid and resid of the first cysteine (CYS A). *}
{* Second 2 entries are the segid and resid of the second cysteine (CYS B). *}
{+ table: rows=8 numbered
cols=5 "use" "segid CYS A" "resid CYS A" "segid CYS B" "resid CYS B" +}
{+ choice: true false +}
{===>} ss_use_1=true;
{===>} ss_i_segid_1="A"; ss_i_resid_1=32;
{===>} ss_j_segid_1="B"; ss_j_resid_1=112;
There is one file generated: an MTF file (this contains the molecular topology information which describes to covalent topology of the molecule).