[gmx-users] Atom index overflow after adding water

[Peggy Yao]

Thank you, Justin!

I changed the output files to .gro.

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

However, the overflow error still occurs in the gro file:

32448SOL    HW299996   9.410   8.282   1.575
32449SOL     OW99997   9.923   8.813   0.726
32449SOL    HW199998   9.874   8.726   0.735
32449SOL    HW299999   9.900   8.856   0.639
32450SOL     OW    0   0.018   7.452   0.502
32450SOL    HW1    1   0.058   7.543   0.493
32450SOL    HW2    2  -0.082   7.460   0.508
32451SOL     OW    3   9.507   8.424   1.264
32451SOL    HW1    4   9.596   8.379   1.250

What's wrong? Thanks a lot!

Peggy

On Sat, Feb 14, 2009 at 2:40 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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