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

[Justin Lemkul]

On 12/14/16 12:53 AM, Seera Suryanarayana wrote:
> 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?
>

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.

> 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.
>

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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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