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

[Justin Lemkul]

On 12/16/16 12:33 AM, Seera Suryanarayana wrote:
> 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
>

This still isn't right.  You've got TH1 residues (which don't exist) and 
mis-named H atoms.  If you want free help, you've got to make it easy.  I don't 
have time to fix several layers of errors to try to get to the root cause.  I 
need to know exactly what you're using to exactly reproduce a problem.

-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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