In picture given atom and atom type ,what type of naming is it and how i can make this sort of naming from my structure ,what is this A and B etc...
I'm from a physics background and I am not aware of this chemistry stuff
The GROMACS manual has all the details of the required format. In short, the format of an [atoms] directive of an .rtp is:
atom name, atom type, charge, charge group
The names can be whatever you like. For HSP, that is a fully protonated histidine, with conventional atom naming.
Justin thanks for your replays,
i know the structure and formate but this naming i could t find anywhere in chemistry.
so i want to know from where i can learn this naming system
in case here first is nitrogen N then in second column what is the meaning of that
NH1 and second is HN and H !!!
no hint for me!
Atom types are specific to force fields, following whatever convention they use. For NH1, it is an N attached to 1 hydrogen, hence NH1. HA is aliphatic hydrogen, etc. The atomtypes.atp file has comments on all of these.
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