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definition of ASN
- dark_angel83
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11 years 1 month ago #1476
by dark_angel83
definition of ASN was created by dark_angel83
Dear MARTINI developers,
i am reading martinize code and I don't understand why, in the mapping dictionary, ASN is defined as
"ASN": nsplit(bb,"CB CG ND1 ND2 OD1 OD2 HD11 HD12 HD21 HD22")
ASN is supposed to have only one nitrogen in the side chain, isn't it?
Francesco
i am reading martinize code and I don't understand why, in the mapping dictionary, ASN is defined as
"ASN": nsplit(bb,"CB CG ND1 ND2 OD1 OD2 HD11 HD12 HD21 HD22")
ASN is supposed to have only one nitrogen in the side chain, isn't it?
Francesco
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- xavier
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11 years 1 month ago #1477
by xavier
Replied by xavier on topic definition of ASN
You are correct. The nitrogen is ND2. It is however not a problem is the atom does not exist it won't be included.
The presence of both names might result from that the person who wrote the code was not sure if the name was ND1 or ND2 and thus included then both, or that in fact in some cases in the PDB files ND1 is used instead of ND2, or in some force fields it might also happen ... many reasons but you should not worry about it.
The presence of both names might result from that the person who wrote the code was not sure if the name was ND1 or ND2 and thus included then both, or that in fact in some cases in the PDB files ND1 is used instead of ND2, or in some force fields it might also happen ... many reasons but you should not worry about it.
dark_angel83 wrote: Dear MARTINI developers,
i am reading martinize code and I don't understand why, in the mapping dictionary, ASN is defined as
"ASN": nsplit(bb,"CB CG ND1 ND2 OD1 OD2 HD11 HD12 HD21 HD22")
ASN is supposed to have only one nitrogen in the side chain, isn't it?
Francesco
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