[gmx-users] How to merge 2 top-files

[Mark Abraham]

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: greendreams1983 at 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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