Number of atoms in pdb file not matching topology file

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1

GROMACS version:
GROMACS modification: Yes/No
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When I tried gmx pdb2gmx script for creating topology file for my protein containing 5013 atoms using gromos53_a6 forcefield , it generated topology for only 3145 atoms instead of 5013 . Why did it miss the other atoms. The mysterious part is that the software didn’t give aby error message . When I tried creating the topology file using charmm forcefield, it gave me proper results . But the problem is that I want to lipid membrane protein complex simulation, and according to the tutorial , I have to use gromos53_a6 forcefield . What should I do ?
Can anyone please help me in this regard

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This pic shows the warning that the software gives without running into a fatal error

2

The GROMOS force fields are united atom force fields. I guess there are non-polar hydrogens in the pdb file. Does it help if you use the -ignh option with gmx pdb2gmx?

Edit: You will then also need to use the -o option to get a .gro file with the correct hydrogen count.