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

[Justin A. Lemkul]

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?
> 

What was your genion command line?  Did you specify, i.e. genion -pname Na 
-nname Cl?  The names you give genion should match the atom names you find in 
ions.itp, which for OPLS should be NA+ and CL- (Na and Cl are for ffgmx).

-Justin

> Thanks. I appreciate your time.
> SDA
> 
> 
> 
> 
> 
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-- 
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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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