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

[Peter C. Lai]

In this case,
Can't you just use pdb2gmx to regenerate the topology file from the merged
gro which will resolve the separate moleculechains for you?        

On 2011-03-30 04:25:34AM -0500, Mark Abraham wrote:
> 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<mailto: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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Peter C. Lai                 | University of Alabama-Birmingham
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