Molecule

Use of the molecule file

.

Attribute list

The attributes present in the file are:

• 'name' is used to define the root name of structure files produced by ARIA. In the example given below, the file names will be: prot_xx.pdb, where xx is the generation rank.
  
• "chain_type" can be now: PROTEIN (other possibilities?). This attribute determines the topology and parameters files used in the structure calculation. PROTEIN corresponds to the set of files: parallhdg5.2.pro, topallhdg.pep and topallhdg5.2.pro.

• 'molecule_segid' defines the chain name. The default value is for only one chain (for a dimer, see the example page http...). Be careful to use a four-character string with the chain letter at the most right character.The chain ids are generally numbered as: '   A', '   B', '   C' etc...
• 'residue-type' defines the type of amino-acid or base
• 'number' is the residue number
• An atom contains the attributes: 'atom_type' and 'hetero_name' which is the name of the heavy atom to which the atom hydrogen is bonded (a verifier).
• At the end of the residue, the groups of equivalent spins are defined. The attribute group_type ('METHYL', 'METHYLENE',  'NTERMINUS', 'ISOPROPYL', 'AROMATIC') determines the assignment of chemical shifts to the hydrogens.
  

Example of file

The format of an XML molecule file is given below for the tripeptide PHE-MET-IILE-GLY.

<!DOCTYPE molecule SYSTEM "molecule1.0.dtd">
  <molecule name="prot">
  <chain chain_type="PROTEIN" segid="   A" structure=""> 
    <residue residue_type="PHE" number="1">
      <atom name="C" atom_type="C" hetero_name=""/>
      <atom name="CA" atom_type="C" hetero_name=""/>
      <atom name="CB" atom_type="C" hetero_name=""/>
      <atom name="CD1" atom_type="C" hetero_name=""/>
      <atom name="CD2" atom_type="C" hetero_name=""/>
      <atom name="CE1" atom_type="C" hetero_name=""/>
      <atom name="CE2" atom_type="C" hetero_name=""/>
      <atom name="CG" atom_type="C" hetero_name=""/>
      <atom name="CZ" atom_type="C" hetero_name=""/>
      <atom name="H1" atom_type="H" hetero_name="N"/>
      <atom name="H2" atom_type="H" hetero_name="N"/>
      <atom name="H3" atom_type="H" hetero_name="N"/>
      <atom name="HA" atom_type="H" hetero_name="CA"/>
      <atom name="HB2" atom_type="H" hetero_name="CB"/>
      <atom name="HB3" atom_type="H" hetero_name="CB"/>
      <atom name="HD1" atom_type="H" hetero_name="CD1"/>
      <atom name="HD2" atom_type="H" hetero_name="CD2"/>
      <atom name="HE1" atom_type="H" hetero_name="CE1"/>
      <atom name="HE2" atom_type="H" hetero_name="CE2"/>
      <atom name="HZ" atom_type="H" hetero_name="CZ"/>
      <atom name="N" atom_type="N" hetero_name=""/>
      <atom name="O" atom_type="O" hetero_name=""/>
      <equivalent_group group_type="AROMATIC">
        <atom_name name="HD1"/>
        <atom_name name="HD2"/>
      </equivalent_group>
      <equivalent_group group_type="AROMATIC">
        <atom_name name="HE1"/>
        <atom_name name="HE2"/>
      </equivalent_group>
      <equivalent_group group_type="METHYLENE">
        <atom_name name="HB2"/>
        <atom_name name="HB3"/>
      </equivalent_group>
      <equivalent_group group_type="AROMATIC">
        <atom_name name="HD1"/>
        <atom_name name="HD2"/>
        <atom_name name="HE1"/>
        <atom_name name="HE2"/>
        <atom_name name="HZ"/>
      </equivalent_group>
      <equivalent_group group_type="NTERMINUS">
        <atom_name name="H1"/>
        <atom_name name="H2"/>
        <atom_name name="H3"/>
      </equivalent_group>
     </residue>
    <residue residue_type="MET" number="2" structure="">
      <atom name="C" atom_type="C" hetero_name=""/>  
      <atom name="CA" atom_type="C" hetero_name=""/> 
      <atom name="CB" atom_type="C" hetero_name=""/>
      <atom name="CE" atom_type="C" hetero_name=""/> 
      <atom name="CG" atom_type="C" hetero_name=""/> 
      <atom name="H1" atom_type="H" hetero_name="N"/> 
      <atom name="H2" atom_type="H" hetero_name="N"/> 
      <atom name="H3" atom_type="H" hetero_name="N"/> 
      <atom name="HA" atom_type="H" hetero_name="CA"/> 
      <atom name="HB2" atom_type="H" hetero_name="CB"/>
      <atom name="HB3" atom_type="H" hetero_name="CB"/> 
      <atom name="HE1" atom_type="H" hetero_name="CE"/>
      <atom name="HE2" atom_type="H" hetero_name="CE"/>
      <atom name="HE3" atom_type="H" hetero_name="CE"/>
      <atom name="HG2" atom_type="H" hetero_name="CG"/>
      <atom name="HG3" atom_type="H" hetero_name="CG"/> 
      <atom name="N" atom_type="N" hetero_name=""/> 
      <atom name="O" atom_type="O" hetero_name=""/> 
      <atom name="SD" atom_type="S" hetero_name=""/> 
      <equivalent_group group_type="METHYL"> 
        <atom_name name="HE1"/> 
        <atom_name name="HE2"/> 
        <atom_name name="HE3"/>
      </equivalent_group> 
      <equivalent_group group_type="METHYLENE"> 
        <atom_name name="HB2"/> 
        <atom_name name="HB3"/>
      </equivalent_group> 
      <equivalent_group group_type="METHYLENE">
        <atom_name name="HG2"/>
        <atom_name name="HG3"/> 
      </equivalent_group>
      <equivalent_group group_type="NTERMINUS">
        <atom_name name="H1"/> 
        <atom_name name="H2"/> 
        <atom_name name="H3"/>
      </equivalent_group> 
    </residue> 
    <residue residue_type="VAL" number="3" structure="">
      <atom name="C" atom_type="C" hetero_name=""/>
      <atom name="CA" atom_type="C" hetero_name=""/>
      <atom name="CB" atom_type="C" hetero_name=""/>
      <atom name="CG1" atom_type="C" hetero_name=""/>
      <atom name="CG2" atom_type="C" hetero_name=""/>
      <atom name="H" atom_type="H" hetero_name="N"/>
      <atom name="HA" atom_type="H" hetero_name="CA"/>
      <atom name="HB" atom_type="H" hetero_name="CB"/>
      <atom name="HG11" atom_type="H" hetero_name="CG1"/>
      <atom name="HG12" atom_type="H" hetero_name="CG1"/>
      <atom name="HG13" atom_type="H" hetero_name="CG1"/>
      <atom name="HG21" atom_type="H" hetero_name="CG2"/>
      <atom name="HG22" atom_type="H" hetero_name="CG2"/>
      <atom name="HG23" atom_type="H" hetero_name="CG2"/>
      <atom name="N" atom_type="N" hetero_name=""/>
      <atom name="O" atom_type="O" hetero_name=""/>
      <equivalent_group group_type="ISOPROPYL">
        <atom_name name="HG11"/>
        <atom_name name="HG12"/>
        <atom_name name="HG13"/>
        <atom_name name="HG21"/>
        <atom_name name="HG22"/>
        <atom_name name="HG23"/>
      </equivalent_group>
      <equivalent_group group_type="METHYL">
        <atom_name name="HG21"/>
        <atom_name name="HG22"/>
        <atom_name name="HG23"/>
      </equivalent_group>
      <equivalent_group group_type="METHYL">
        <atom_name name="HG11"/>
        <atom_name name="HG12"/>
        <atom_name name="HG13"/>
      </equivalent_group>
    </residue>
    <residue residue_type="GLY" number="4">
      <atom name="C" atom_type="C" hetero_name=""/>
      <atom name="CA" atom_type="C" hetero_name=""/>
      <atom name="H" atom_type="H" hetero_name="N"/>
      <atom name="HA2" atom_type="H" hetero_name="CA"/>
      <atom name="HA3" atom_type="H" hetero_name="CA"/>
      <atom name="N" atom_type="N" hetero_name=""/>
      <atom name="O'" atom_type="O" hetero_name=""/>
      <atom name="O''" atom_type="O" hetero_name=""/>
      <equivalent_group group_type="METHYLENE">
        <atom_name name="HA2"/>
        <atom_name name="HA3"/>
      </equivalent_group>
    </residue>
   </chain>