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

[Justin Lemkul]

On 12/15/16 4:27 AM, Seera Suryanarayana wrote:
> Dear gromacs users,
>
> 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 pdb2gmx  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/0B5HyqLWajWjHalJ0N0lFSEhHcmM/view?usp=drive_web
>
>  Kindly help me how to solve it?
>

I get a different error:

-------------------------------------------------------
Program gmx, VERSION 5.0
Source code file: 
/Users/justin/Downloads/gromacs-5.0/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 732

Fatal error:
Atom P01 in residue THR 26 was not found in rtp entry THR with 14 atoms
while sorting atoms.
.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

THR is not the correct phosphorylated residue name, and P01 is not a valid atom 
name.  You need to re-name the residues and atoms as needed to conform to the 
force field's requirements.  Check the CHARMM36 merged.rtp file; I have the 
residues labeled with explicit comments like "monoanionic phosphoserine," 
"dianionic phosphoserine," etc.

If you have a correct file that exactly reproduces the problem you've posted 
above, I will take another look at that.

-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

==================================================