[gmx-users] Error regarding pdb2gmx of modified residue

[Mark Abraham]

Hi,

I would rename those atoms exactly as the .tdb file in your force field
expects. And if that doesn't work, try deleting them and having pdb2gmx
rebuild them.

Mark

On Mon, Jan 1, 2018 at 5:53 AM Amir Zeb <zebamir85 at gmail.com> wrote:

> Hi gmx users,
>
> Wishing you all a very happy new year 2k18.
>
> I have modified a particular Tyr residue to phosphorylated Tyr and renamed
> as TP2 per forcefield recognizable name. I have used:
> gmx pdb2gmx -f xxx.pdb -o xxx.gro -ignh -ter (as full command)
> C36m ff
> Gromacs v5.0.6
> NH3+ as N-terminus
> COO- as C-terminus
> TIP3P water model
>
> I am getting error:
>
> Fatal error:
> Atom OXT in residue SER 287 was not found in rtp entry SER with 11 atoms
> while sorting atoms.
>
> The C-terminus of my pdb file is pasted right here:
> ATOM   4538  OC1 SER A 287
> ATOM   4539  OC2 SER A 287
> TER      4540           SER A 287
> END
>
> I am aware of that SER 287 is C-terminus residue but by which name should i
> replace the terminal oxygen to cope with this error?
>
> Looking forward for your kind suggestions.
>
> Thanks in advance!
>
> ~Amir
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