[gmx-users] Error regarding pdb2gmx of modified residue

Amir Zeb zebamir85 at gmail.com
Mon Jan 1 06:52:42 CET 2018

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

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!


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