[gmx-users] editying top file after solvation
Justin A. Lemkul
jalemkul at vt.edu
Sat Aug 21 21:11:38 CEST 2010
jojo J wrote:
> 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
You don't include a .top within a .top. You include an .itp within a .top,
otherwise you'll get all kinds of errors related to the fact that the topology
file format will be severely broken.
> 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).
You should only set all charges to zero if that's an appropriate model. I can
hardly think of a case where that would be appropriate...
> 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..
You need to spend some time with the manual, Chapter 5. Your solute and solvent
should be separate [moleculetype] directives, for which all atom number is
sequential and starts from zero. Do any of the basic tutorials and look at how
this is done for a simple protein in water. Of particular educational value
would be the grompp-processed topology (grompp -pp), which will show you the
entire contents of the topology, expanded based on everything that was #included.
> Thanks for your help,
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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