[gmx-users] Atom index overflow after adding water

[Mark Abraham]

----- Original Message -----
From: Peggy Yao <peggy.yao at gmail.com>
Date: Sunday, February 15, 2009 10:24 am
Subject: Re: [gmx-users] Atom index overflow after adding water
To: jalemkul at vt.edu, Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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!

Probably nothing. The issue is whether the parsing algorithm in grompp will handle the situation gracefully. Justin thinks it does. You should try it and see :-)

Mark