[gmx-users] Atom O in residue was not found in rtp entry

[Justin Lemkul]

On 12/15/19 11:01 AM, Sadaf Rani wrote:
> Dear Gromacs users
> I have a ligand in my protein for which I make rtp file and included this
> in my local copy for force field as mentioned in gromacs manual. Also, I
> added atom types in ffnonbonded.itp and atomtypes.atp atomtypes.atp added
> residue under protein in residuetypes.dat
> But I am getting the following error:-
>
>
> Splitting chemical chains based on TER records or chain id changing.
> WARNING: Chain identifier 'A' is used in two non-sequential blocks.
> They will be treated as separate chains unless you reorder your file.
> There are 2 chains and 0 blocks of water and 490 residues with 7921 atoms
>
>    chain  #res #atoms
>    1 'A'   489   7894
>    2 'A'     1     27
>
> All occupancies are one
> Opening force field file ./amber99sb-ildn.ff/atomtypes.atp
> Atomtype 86
> Invalid format:
>
>
> ------------------------------------------------------
> Program:     gmx pdb2gmx, version 2019.4
> Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 745)
>
> Fatal error:
> Atom O in residue G6P 516 was not found in rtp entry G6P with 27 atoms
> while sorting atoms.
>
>
> Could you please suggest me what wrong I am doing in rtp file

If your G6P residue in the coordinate file has an atom named "O," this 
does not appear in the .rtp file and you should rename the atom in the 
coordinate file so that it is in agreement with the .rtp file. If your 
G6P does not have anything simply named "O" then you are likely seeing a 
side effect of the xlateat.dat interpreting your residue as protein and 
replacing "O1" with "O." In this case, either (1) do not specify G6P as 
"Protein" in residuetypes.dat or rename the O1 atom in the .rtp entry 
and coordinate file.

-Justin

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Justin A. Lemkul, Ph.D.
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