[gmx-users] Error regarding pdb2gmx of modified residue
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)
NH3+ as N-terminus
COO- as C-terminus
TIP3P water model
I am getting 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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