[gmx-users] error in pdb2gmx

[Sadaf Rani]

Dear Gromacs users
I am facing a strange problem while doing pdb2gmx:-
When I use the command:-
 gmx pdb2gmx -f 74A-G.pdb -o 74A-G.gro
It shows the following:-
going to rename ./amber99sb-ildn.ff/aminoacids.r2b
Opening force field file ./amber99sb-ildn.ff/aminoacids.r2b
going to rename ./amber99sb-ildn.ff/dna.r2b
Opening force field file ./amber99sb-ildn.ff/dna.r2b
going to rename ./amber99sb-ildn.ff/rna.r2b
Opening force field file ./amber99sb-ildn.ff/rna.r2b
Reading 74A-G.pdb...
Read '', 4082 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 2 chains and 0 blocks of water and 492 residues with 4082 atoms

  chain  #res #atoms
  1 'A'   489   3970
  2 'B'     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: ''

However, when I use without gmx, as below:-
pdb2gmx -f 74A-G.pdb -o 74A-G.gro
It generates topology file successfully. What's wrong with the format in
atomtypes.atp I am unable to understand. Could you please help me to find
out?
I have added a new residue to my forcefield file as mentioned in gromacs
manual.
Please correct me where I am wrong, I have added following in
atomtypes.atp file:-
;[ 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

Thanks.

Sadaf