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.
http://www.gromacs.org/Documentation/Tutorials#General
-Justin
-
Thanks for your help,
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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