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

[Mark Abraham]

Hi,

I suggest you produce your initial conformation in .gro format, which
permits five-character atom names. That might mean using editconf on your
.pdb file, and then manually renaming atoms.

Mark

On Fri, Jun 23, 2017 at 3:55 AM Qing Lv <lvqingjiejie at 163.com> wrote:

> 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
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