[gmx-users] Problems with ion names in OPLS and gromacs 4.0.2

Mark Abraham Mark.Abraham at anu.edu.au
Mon Nov 17 13:03:02 CET 2008

DimitryASuplatov wrote:
> Hello,
> I want neutralize negative charge in my structure. I use genion to add
> 80 Na and 71 Cl. Than I edit top file manually to decrease SOL number by
> 151 and add two lines for ions. Since I use OPLSAA they should look like
> this (considering names in gromacs/share/gromacs/top/ions.itp)
> NA+             80
> CL-             71
> When I run grompp afterwards I receive this message:
> --------------------------------------------------------
> Warning: atom name 105260 in 1klc_final_frc.top and
> 1klc_final_frc.si.gro does not match (NA - Na)
> Warning: atom name 105261 in 1klc_final_frc.top and
> 1klc_final_frc.si.gro does not match (NA - Na)
> (more than 20 non-matching atom names)
> WARNING 1 [file 1klc_final_frc.top, line 42]:
>   151 non-matching atom names
>   atom names from 1klc_final_frc.top will be used
>   atom names from 1klc_final_frc.si.gro will be ignored
> --------------------------------------------------------
> That was expected since gro file identifies the ions as "Na" and "Cl",
> but this is the first time in my experience when grompp throws out this:
> -------------------------------------------------------
> Program grompp, VERSION 4.0.2
> Source code file: gmx_fatal.c, line: 481
> Fatal error:
> Too many warnings (1), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> -------------------------------------------------------
> Is this a problem or should I simply set -maxwarn to 2?

Since GROMACS 4, any warning causes grompp to fail, since it was felt 
that too often inexperienced users don't go and read ones that they 
should have paid attention to. There are multiple work-arounds for your 
problem - use genion more cunningly as Justin suggested, or do a text 
search-and-replace in your .gro file. Getting in the habit of setting 
-maxwarn runs the risk of missing real warnings later. Unless it's 
onerous, fix the causes, not the symptoms. :-)


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