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4.4 PATCH — Patches Special Structures

4.4.1 Syntax

     PATCh HEME [NBXMod int]
     PATCh LIGA [NBXMod] int]

4.4.2 Function

PATCH HEME is used to patch the ligation of a histidine to a heme residue. The histidine-heme-spec is a pair of integers read by a format of 2I5, IRES and JRES, are the residue numbers of the histidine and heme, respectively. The bond is formed between the NE2 of the histidine and FE of the HEME. For each bond formed, additional bond angles, torsion angles, and non-bonded exclusions are added.

PATCH LIGAND is used to patch the ligation of a carbon monoxide to a heme. The carbon monoxide-heme-histidine-spec consists of three integers, read by a format of 3I5, and again are not free format. The three numbers refer to the histidine, heme, and CO residue numbers respectively. This patch takes care of the carbon monoxide heme bond. It should be called after PATCH HEME is called.

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

WARNING: This code has been tested only with the extended atom topology file. It may not work for current editions of the other amino acid topology files, and it will not work if there is a proton placed on the NE2 of the histidine.

It is not possible to patch any interaction involving atoms of a symmetric image using these command (see Images).