[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
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list