[gmx-users] problem in making topology file for protein inlipid bilayer

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 23 15:33:05 CEST 2009

nitu sharma wrote:
> Dear Mark
> Thanks for your consideration.
> I am replying you again I think it will be more easy for u in 
> understanding my problem.
> as u ask- how many atoms is------Protein A- 5244
>                                                  Protein B- 4658
>          And in one dmpc molecule there is 46 atoms  so in 128 it is 5888
> atoms

That's information for you to make deductions with, not me. :-) You had 
9K atoms in your coordinate file, so you've made some large mistake 

>  > can u suggest me how it is helpful in making correct topology file.
> As you wrote in your mail you should make two # ifdef POSRES section does it
> means separatly before addind .itp file of Protein A and Protein B????????

Read chapter 5 and understand how a [moleculetype] works. There's a 
reason there's an example .itp file listed there.


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