[gmx-users] Atom index overflow after adding water

[Peggy Yao]

Dear all,

Has anyone encountered the problem of atom index overflow in PDB files after
adding water molecules?

The following are what I did:

pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o 1eia.pdb -water
spce >& pdb2gmx.log
# add water
editconf -bt cubic -f 1eia.pdb -o 1eia.pdb -c -d 0.9 >& editconf.log
genbox -cp 1eia.pdb -cs spc216.gro -o 1eia_water.pdb -p 1eia.top >&
genbox.log

However, in 1eia_water.pdb, the atom index of the water section overflowed:

ATOM  99996  HW2 SOL  2448      98.583  52.132  64.542  1.00  0.00
ATOM  99997  OW  SOL  2449       1.182  45.201  68.242  1.00  0.00
ATOM  99998  HW1 SOL  2449       1.592  44.881  69.102  1.00  0.00
ATOM  99999  HW2 SOL  2449       0.222  44.931  68.212  1.00  0.00
ATOM      0  OW  SOL  2450      93.503  42.681  67.002  1.00  0.00
ATOM      1  HW1 SOL  2450      94.353  42.351  66.592  1.00  0.00
ATOM      2  HW2 SOL  2450      93.633  42.831  67.982  1.00  0.00
ATOM      3  OW  SOL  2451      94.993  42.441  73.082  1.00  0.00

How to solve this problem?

Thanks,
Peggy
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