[gmx-users] editying top file after solvation

jojo J joojoojooon at gmail.com
Sat Aug 21 21:02:36 CEST 2010

Dear gmx users,

I am solvating a solute with a solvent molecule using command line below:

genbox -cp solute.gro -cs solvent.gro -o solvated.gro -p solute.top

solute is in a 20nm cubic box and by this command I am getting solvated box.
solute.top is the top file of solute. I searched the archive list on how to
edit top file for the next step which is EM of solvated molecule. I dont
know how to include solvent.top file in solute.top. To do EM somehow I need
to provide ff parameters of my solvent right? (also I wan to set zero
charges ot all atoms so I need to do this before EM).

I copied the solvent.top contents is solute top file but since atoms numbers
are identical grompp em gives non atom match names error. Could you tell me
what shoudl be in the [moleculetype] directory and last directory in
solute.top for EM? Also I think I have to pay attention to number of solvent
molecules in solvated.gro file and include it in top file I think..


Thanks for your help,
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