[gmx-users] Atom index overflow after adding water

[Justin A. Lemkul]

Peggy Yao wrote:
> 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:
> 

Probably.  Search the entire output of grompp for the error message.  I don't 
remember grompp ever reporting a fatal error without printing the actual problem 
somewhere that the user can see.

If you can provide that information, as well as the contents of your .mdp, there 
may be a chance to diagnose what's going on.  As I said before, the problem 
*shouldn't* be the number of atoms in the file.

-Justin

> 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 
> <mailto:mark.abraham at anu.edu.au>> wrote:
> 
> 
> 
>     ----- Original Message -----
>     From: Peggy Yao <peggy.yao at gmail.com <mailto: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 <mailto:jalemkul at vt.edu>, Discussion list for
>     GROMACS users <gmx-users at gromacs.org <mailto: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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-- 
========================================

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

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