[gmx-users] Atom index overflow after adding water

[Peggy Yao]

Unfortunately, no. :( When I tried to add ions to the system using:

grompp -f em.mdp -c 1eia_water.gro -p 1eia.top -o 1eia_ion.tpr

It return me an error without explanation:

processing coordinates...
double-checking input for internal consistency...

There was 1 note

-------------------------------------------------------
Program grompp, VERSION 4.0.2
Source code file: grompp.c, line: 864

Fatal error:
There were 1 error(s) processing your input
-------------------------------------------------------

Did I make any mistake? I am new to MD simulation and Gromacs. The following
are all the steps that I ran until the fatal error:

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
# add counter ions
grompp -f em.mdp -c 1eia_water.gro -p 1eia.top -o 1eia_ion.tpr >&
grompp_ion.log

Peggy

On Sat, Feb 14, 2009 at 3:31 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> ----- 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
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