ADD_TPG SOLUTE

NAME
ADD_TPG SOLUTE - Add topology components to the current solute molecule

SYNOPSIS

ADD_TPG SOLUTE
    ...
    ...
END

DESCRIPTION
The structured command ADD_TPG SOLUTE opens an environment including commands which add extra bonds, proper and improper torsions to the topology of the current solute molecule(s). The command is closed by END. This command must be used to connect atoms belonging to different residues of the current molecule. For instance to connect through a sulfur bridge two cysteine residues or to bind ligands to a metal atom.

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bond  1ata 2atb    residue   num1 num2
Add a bond to the topology of the current solute molecule which connect atom ata of residue number num1 with atom atb of residue number num2. The number 1 and 2 refer to residue num1 and num2, respectively. The atom label ata and atb must be defined in the general formatted topology file as labels of actual atoms of residue number num1 and num2. Here, residue numbers are the sequential numbers of the residues as given in input to command JOIN.

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torsion  1ata 1atb 2atc 2atd    residue   num1 num2
Add a proper torsion to the topology of the current solute molecule. The number 1 and 2 refer to residue num1 and num2, respectively. Atom ata and atb belong to residue number num1, while atoms atc and atd are on residue number num2. Additional torsion having three atoms on one residue and one atom on the other residue are also allowed. Here, residue numbers are the sequential numbers of the residues as given in input to command JOIN. If the command AUTO_DIHEDRAL of the environment &SOLUTE is used, no extra torsions need to be added to the current topology.

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i_torsion  1ata 1atb 2atc 2atd    residue   num1 num2
Add an improper torsion to the topology of the current solute molecule. The number 1 and 2 refer to residue numbers num1 and num2, respectively. Atom ata and atb belong to residue number num1, while atoms atc and atd are on residue number num2. Additional improper torsions having three atoms on one residue and one atom on the other residue are also allowed. Here, residue numbers are the sequential numbers of the residues as given in input to command JOIN.

EXAMPLES

ADD_TPG SOLUTE
     bond 1sg 2sg residue 6 127
     bond 1sg 2sg residue 30 115
     bond 1sg 2sg residue 64 80
     bond 1sg 2sg residue 76 94
END

Add extra bonds to the current topology. In this example, the four sulfur bridges of hen egg lysozyme are given.

WARNINGS
This command is inactive when used in conjunction with READ_TPGPRM. To have the desired effect, the ADD_TPG environment must be used in conjunction with READ_TPG_ASCII and READ_PRM_ASCII.