28 April 2020 3 2K Report

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?

Thanks in advance.

Sadaf

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