Peggy Yao wrote:
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?
Well, the .pdb file format can only handle a fixed amount of digits when
numbering atoms. I don't know if using .gro format will be of any use, but I
routinely simulate systems of 200,000+ atoms with no problem, and any index
files I make are correctly numbered.
-Justin
Thanks,
Peggy
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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