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 <[email protected]
<mailto:[email protected]>> wrote:
----- Original Message -----
From: Peggy Yao <[email protected] <mailto:[email protected]>>
Date: Sunday, February 15, 2009 10:24 am
Subject: Re: [gmx-users] Atom index overflow after adding water
To: [email protected] <mailto:[email protected]>, Discussion list for
GROMACS users <[email protected] <mailto:[email protected]>>
> 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
========================================
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