Dear all,<br><br>Has anyone encountered the problem of atom index overflow in PDB files after adding water molecules?<br><br>The following are what I did:<br><br>pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o 1eia.pdb -water spce >& pdb2gmx.log<br>
# add water<br>editconf -bt cubic -f 1eia.pdb -o 1eia.pdb -c -d 0.9 >& editconf.log<br>genbox -cp 1eia.pdb -cs spc216.gro -o 1eia_water.pdb -p 1eia.top >& genbox.log<br><br>However, in 1eia_water.pdb, the atom index of the water section overflowed:<br>
<br>ATOM 99996 HW2 SOL 2448 98.583 52.132 64.542 1.00 0.00<br>ATOM 99997 OW SOL 2449 1.182 45.201 68.242 1.00 0.00<br>ATOM 99998 HW1 SOL 2449 1.592 44.881 69.102 1.00 0.00<br>ATOM 99999 HW2 SOL 2449 0.222 44.931 68.212 1.00 0.00<br>
ATOM 0 OW SOL 2450 93.503 42.681 67.002 1.00 0.00<br>ATOM 1 HW1 SOL 2450 94.353 42.351 66.592 1.00 0.00<br>ATOM 2 HW2 SOL 2450 93.633 42.831 67.982 1.00 0.00<br>ATOM 3 OW SOL 2451 94.993 42.441 73.082 1.00 0.00<br>
<br>How to solve this problem?<br><br>Thanks,<br>Peggy<br>