On 30/03/2011 8:14 PM, Ghassen Hassani wrote:
Dear Friends,
Right now i am working on the docking of a small ligand to a receptor.
in order to begin md simulations in gromacs, i need to create some files..
I have already docked my ligand to the receptor and i have those files:
- ligand_receptor.gro
- posre.itp (for only the receptor !!)
I have 2 Questions:
1- How can i expand the posre.itp file to also include the ligand.data ?
Don't. The position restraints file is intended to be #included from
within a [moleculetype]. You have two, so you need two position
restraint files, each #included from a different, appropriate place. The
GROMACS tool genrestr can help generate that for the ligand.
that means how can i do to create a posre.itp-file for my
ligand_receptor-komplex ?
Don't.
2- I have 2 separate top-files: ligand.top (from the prodrg-server)
and the receptor.top file. How can i "merge" the 2 files and obtain
the file ligand_receptor.top for the whole ligand-receptor-komplex ?
You need to convert one of your [moleculetype] definitions in one of
your .top files into an .itp file
(http://www.gromacs.org/Documentation/File_Formats/.itp_File) and
#include it suitably from the other. See chapter 5 of the manual for
details. This is tricky, do your homework first. Note that you should
take note of the warning here:
http://www.gromacs.org/Downloads/Related_Software/PRODRG
Many thanx, please email-me on my adress: greendreams1...@yahoo.de
Yours.
No, that is against accepted netiquette. If your question is worth
answering, then that answer is worth broadcasting and archiving so
others can learn from it.
Mark
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