[gmx-users] How to solve OXT atom (termial oxygen atom) issue?

[Seera Suryanarayana]

First of all I am extremely sorry for my mistake. I haven't sent you the
modified coordinate file.

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 field.
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.

  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?


Internally, pdb2gmx re-maps any reference to the OXT atom to one named
OT2.  No changes are made to the .rtp file and you certainly don't need to
change anything.


Please upload your coordinate file somewhere and provide a URL.  I cannot
reproduce the problem with a simple test system.  A peptide that I have
with a  C-terminal GLN works fine with either O/OXT or OT1/OT2.

-Justin

As Justin asked me coordinate file, I have provided below the link of my
coordinate file

https://drive.google.com/file/d/0B5HyqLWajWjHU3J3RW9PalhKZ1E/view?usp=drive_web



Surya
Graduate student
India.