[gmx-users] How to solve the OXT atom (terminal O atom) issue?

[Seera Suryanarayana]

Dear gromacs users,

I have peptide with 68 residues and some of the SER and THR residues
are phosphorylated. I have chosen charmm36 force field. When I
executed the pdb2gmx  I got following error.

Fatal error:
Atom OXT in residues GLN 68 was not found un rtp enrty GLN with 17
atoms while sorting atoms.

I have checked the rtp file and it does not have the terminal oxygen
atom GLN. Then I have checked c.tdb file and I found the following
information.

[ None ]

; CHARMM CTER
[ COO- ]

[ replace ]
 C           C     CC    12.011      0.34
 O          OT1  OC    15.9994   -0.67
 OXT      OT2  OC    15.9994   -0.67

[ add ]
 2  8   OT  C   CA  N

   OC  15.9994 -0.67   -1

[ impropers ]
 C  CA  OT2 OT1

What I understand here is that the OXT atom is to be replaced by OT2
and add the information to the rtp file. Am I right?

And also for your information I am giving you terminal residue atom information.

ATOM    526  N   GLN    68      12.276   4.312 -14.581  1.00 75.07           N
ATOM    527  CA  GLN    68      12.290   4.235 -13.157  1.00 75.07           C
ATOM    528  C   GLN    68      11.301   3.123 -12.798  1.00 75.07           C
ATOM    529  O   GLN    68      11.761   2.088 -12.249  1.00 75.07           O
ATOM    530  CB  GLN    68      11.837   5.542 -12.486  1.00 75.07           C
ATOM    531  CG  GLN    68      12.065   5.756 -11.011  1.00 75.07           C
ATOM    532  CD  GLN    68      11.217   4.937 -10.053  1.00 75.07           C
ATOM    533  NE2 GLN    68      11.740   3.726  -9.682  1.00 75.07           N
ATOM    534  OE1 GLN    68      10.121   5.317  -9.679  1.00 75.07           O
ATOM    535  OXT GLN    68      10.085   3.305 -13.052  1.00 75.07           O1-
TER     536      GLN    68

Kindly help me how to solve it.

Thanks in advance,
Surya
Graduate student
India.