[gmx-users] 5-letter atom names in topology files

[Qing Lv]

Hi,


Gromos 54a7 force field has built-in topologies for some small molecules, like ATP. In these topologies, many atoms have names of up to 5 letters, such as AO1PA and AO2PB. However, PDB files seem do not support 5-letter atom names. So, if I name an atom "AO2PB" in PDB, it will be truncated to "AO2P" or "O2PB" when executing pdb2gmx, and these atoms cannot be recognized then.
Anyone know how to solvate this problem? Many thanks ^_^


Qing