[gmx-users] Invalid atomtype format

[Justin Lemkul]

On 4/28/20 11:52 AM, Sadaf Rani wrote:
> Dear Gromacs users
> I am facing a problem between different versions of gromacs for gmx
> pdb2gmx. I have a protein-ligand system, I did all the necessary steps
> mentioned in gromacs manual for adding new residue to force field. When I
> run this in gromacs 2019 it gives me a warning as below:-
> Fatal error:
> Invalid atomtype format: ''
> But it still generates a gro file and topology. But When I am using gromacs
> 2020, I get the same message of invalid atomtype format as below:-
>
> Reading 78I-T.pdb...
> WARNING: all CONECT records are ignored
> Read '', 4083 atoms
> Analyzing pdb file
> 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 492 residues with 4083 atoms
>
>    chain  #res #atoms
>    1 'A'   489   3971
>    2 'A'     3    112
>
> All occupancies are one
> Opening force field file ./amber99sb-ildn.ff/atomtypes.atp
>
> -------------------------------------------------------
> Program:     gmx pdb2gmx, version 2020-UNCHECKED
> Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98)
>
> Fatal error:
> *Invalid atomtype format: ''*
>
> I am unable to sort out this problem.
> I have added the atom types of my molecule as mentioned:-
>
> ;[ atomtypes ]
> ; name   bond_type       mass      charge    ptype      sigma      eps
>        nh 14.01000     0.000       A     3.25000e-1   7.11280e-1
>        hn  1.00800     0.000       A     1.06908e-1   6.56888e-2
>        ca 12.01000     0.000       A     3.39967e-1   3.59824e-1
>        nb 14.01000     0.000       A     3.25000e-1   7.11280e-1
>        h5  1.00800     0.000       A     2.42146e-1   6.27600e-2
>        nc 14.01000     0.000       A     3.25000e-1   7.11280e-1
>        cd 12.01000     0.000       A     3.39967e-1   3.59824e-1
>        na 14.01000     0.000       A     3.25000e-1   7.11280e-1
>        c3 12.01000     0.000       A     3.39967e-1   4.57730e-1
>        h2  1.00800     0.000       A     2.29317e-1   6.56888e-2
>        os 16.00000     0.000       A     3.00001e-1   7.11280e-1
>        h1  1.00800     0.000       A     2.47135e-1   6.56888e-2
>        p5 30.97000     0.000       A     3.74177e-1   8.36800e-1
>         o 16.00000     0.000       A     2.95992e-1   8.78640e-1
>        oh 16.00000     0.000       A     3.06647e-1   8.80314e-1
>        ho  1.00800     0.000       A     0.00000e+0   0.00000e+0
>        h4  1.00800     0.000       A     2.51055e-1   6.27600e-2
>         c 12.01000     0.000       A     3.39967e-1   3.59824e-1
>         n 14.01000     0.000       A     3.25000e-1   7.11280e-1
>        ha  1.00800     0.000       A     2.59964e-1   6.27600e-2
>
> Could you please help me to sort out this problem. Even when the format is
> incorrect does it mean that gromacs 2019 is generating a wrong topology?

You should upload a complete test case (including all force field files 
and your PDB structure) somewhere so that we can take a look at it. This 
is a weird error to try to debug. Make sure you're only ever using a 
plain-text editor like VIM or Emacs to avoid inclusion of inappropriate 
characters.

-Justin

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Justin A. Lemkul, Ph.D.
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