[gmx-users] doesn't match coordinate file with topology

[minnale]

Hi users,
     I have generated .gro file of protein by using .xtc file with trjconv command after that i used pdb2gmx command for generating topology file without any error. when I have inserted this protein into popc bilayer by using genbox command i has deleted some of the water and popc molecules, these residues i have mentioned in .top file but when i have used grompp command its showing that 
Fatal error:
 Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (2hel_popc7.6.gro, 12882)
             does not match topology (2hel_noH1.top, 12832)

The same system which is protonated state of protein simulating without generated .gro file by using trjconv command its running fine, But above mentioned system (unprotonated state) showing some fatal error

Couls you pls tell me some suggestion.
Thanks in advance
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