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

[Justin A. Lemkul]

Peter C. Lai wrote:
> 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?        
> 

Only if you really feel like re-writing the ligand topology from scratch as an 
.rtp entry to be processed by pdb2gmx, and then attempt to make a merged 
moleculetype.  In short, yes, it's possible to treat a protein-ligand complex as 
a single entity, but it's probably not worth the effort when it is far simpler 
to #include a ligand topology and #include a position restraint file for it. 
This approach also provides considerably more flexibility in terms of 
restraining the protein and ligand independently, which may be required for 
various applications.

-Justin

> 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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> 

-- 
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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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