[gmx-users] Seeking solution for the error "Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms".

[Santhosh Kumar Nagarajan]

Hi guys,

My problem is in the first step itself.


"Fatal error:
Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms
while sorting atoms."

I understand that the problem is with the .rtp database. But. My doubt
is how to create a new rtp entry for that missing residue.

The following is the portion of my pdb containing the error(OXT).

ATOM    591  N   TRP D 323      10.307  18.558 238.142  1.00 99.84           N
ATOM    592  CA  TRP D 323       9.202  18.123 237.287  1.00101.69           C
ATOM    593  C   TRP D 323       9.168  16.586 237.258  1.00102.94           C
ATOM    594  O   TRP D 323       9.051  16.019 236.150  1.00102.73           O
ATOM    595  OXT TRP D 323       9.259  15.996 238.358  1.00 -1.00           O1-
ATOM    596  CB  TRP D 323       9.296  18.792 235.895  1.00 -1.00           C
ATOM    597  CG  TRP D 323       9.208  20.290 235.866  1.00 -1.00           C
ATOM    598  CD1 TRP D 323       8.072  21.009 235.721  1.00 -1.00           C
ATOM    599  CD2 TRP D 323      10.289  21.267 235.969  1.00 -1.00           C
ATOM    600  NE1 TRP D 323       8.370  22.356 235.739  1.00 -1.00           N
ATOM    601  CE3 TRP D 323      11.693  21.183 236.123  1.00 -1.00           C
ATOM    602  CE2 TRP D 323       9.724  22.577 235.890  1.00 -1.00           C
ATOM    603  CZ3 TRP D 323      12.492  22.342 236.195  1.00 -1.00           C
ATOM    604  CZ2 TRP D 323      10.510  23.741 235.965  1.00 -1.00           C
ATOM    605  CH2 TRP D 323      11.903  23.619 236.118  1.00 -1.00           C
ATOM    606  H   TRP D 323      11.186  18.079 238.010  1.00  0.00           H
ATOM    607  HA  TRP D 323       8.251  18.419 237.732  1.00 -1.00           H
ATOM    608  HB2 TRP D 323      10.221  18.496 235.398  1.00 -1.00           H
ATOM    609  HB3 TRP D 323       8.488  18.416 235.267  1.00 -1.00           H
ATOM    610  HD1 TRP D 323       7.087  20.577 235.614  1.00 -1.00           H
ATOM    611  HE1 TRP D 323       7.661  23.070 235.652  1.00 -1.00           H
ATOM    612  HE3 TRP D 323      12.160  20.211 236.188  1.00 -1.00           H
ATOM    613  HZ3 TRP D 323      13.562  22.249 236.313  1.00 -1.00           H
ATOM    614  HZ2 TRP D 323      10.050  24.715 235.903  1.00 -1.00           H
ATOM    615  HH2 TRP D 323      12.521  24.503 236.177  1.00 -1.00           H

Help me to solve this

Thanks in advance

Regards,
Santhosh