[gmx-users] Atom index overflow after adding water

[Justin A. Lemkul]

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
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

========================================