[gmx-users] Query regarding the addition of solvent molecule

Christina Florina rouvier.florina at gmail.com
Fri Sep 5 08:50:31 CEST 2014

            I have just started my work in MD and using Gromacs 5.0. I need
to use cyclohexane as my solvent instead of water. I generated the topology
file, .itp and .gro using PRODRG. I have successfully incorporated the .gro
file using solvate command and generated the solvent box. But I am facing
problem with grompp (ions.mdp) step before the addition of ions.

gmx grompp -f ions.mdp -c protein_solv.gro -p protein.top -o ions.tpr

            I am getting the FATAL ERROR: NO SUCH MOLECULETYPE CHX  though
I have checked with the molecule name (CHX) in the cyclohexane .itp file. I
have tired changing the name of the molecule also.

           Do I need to add this cyclohexane solvent molecule in the
forcefield file or .atp file, .rtp file? I tried adding them but still not
able to run this. I might be incorrect while adding it in the .rtp file.

            So, I kindly need help regarding the addition of new solvent
molecule in gromacs since I have other organic solvents also for my md work
and having the same problem.

Thank you,

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