Dear All<br><br>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.<br>
<br>The error message was given below.<br><br>Kindly rectify the problem<br>=======================================================================================<br>[student@localhost gro]$ grompp -f em.mdp -p topol.top -c genion.gro -o genem.tpr<br>
<br><br>Ignoring obsolete mdp entry 'cpp'<br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#<br>Generated 332520 of the 332520 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>
Generated 332520 of the 332520 1-4 parameter combinations<br>Excluding 3 bonded neighbours molecule type 'Protein_chain_A'<br>Excluding 2 bonded neighbours molecule type 'SOL'<br><br>-------------------------------------------------------<br>
Program grompp, VERSION 4.5.5<br>Source code file: toppush.c, line: 1987<br><br>Fatal error:<br>No such moleculetype NA+<br>For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>========================================================================================<br><br><br><br>Regards<br><br>Kirubakaran P<br><br>