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

DimitryASuplatov genesup at gmail.com
Mon Nov 17 12:25:30 CET 2008

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?

Thanks. I appreciate your time.

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