[gmx-users] Regarding error in ion neutralization step

kirubakaran palani kirubakaran17 at gmail.com
Fri Nov 4 15:05:56 CET 2011

Dear All

Could any one help me to solve this error in gromacs 4.5.5 version. I am
running dynamics on apo protein and the protein shows negative charge of -6
(after choosing OPLS-AA force filed) and when i was neutralizing the -6
with +6 and generating the genion.tpr file there it shows "No such
moleculetype NA+" error. But the same protein was running with out any
error message in gromacs 4.0.7 version.

The error message was given below.

Kindly rectify the problem
[student at localhost gro]$ grompp -f em.mdp -p topol.top -c genion.gro -o

Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'

Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1987

Fatal error:
No such moleculetype NA+
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Kirubakaran P
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