[gmx-users] How to merge 2 top-files
Mark.Abraham at anu.edu.au
Wed Mar 30 11:25:34 CEST 2011
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 ?
> 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
#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:
> Many thanx, please email-me on my adress: greendreams1983 at yahoo.de
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.
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