[gmx-users] How to resolve OXT atom issue?

Seera Suryanarayana palusoori at gmail.com
Sat Dec 17 07:34:26 CET 2016

Dear Justin,

I apologize you as I am wasting your  valuable time.

  I have peptide with 69 residues and some of the SER and THR residues
  are phosphorylated and also some of the missing residues(1 to 6; 36 to 41
  and 69) have been modeled by modeller . I have chosen charmm36 force
  When I executed the command

  pdb2gmx  -f 1th1.pdb -o 1th1_processed.gro -water spce -ignh

  I got following error.

  Fatal error:

   Atom OXT in residues GLU 69 was not found un rtp enrty GLU with 15
   atoms while sorting atoms.

 Here I am sending a link which has the coordinate file.


Kindly tell me how to solve this error.

Thanks in advance
Graduate student

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