[gmx-users] manually creating a topology file

Mark Abraham mark.abraham at anu.edu.au
Thu Mar 31 12:54:30 CEST 2011

On 31/03/11, Nishith Saurav Topno  <ntopno at bicpu.edu.in> wrote:
> Dear all,
> I intend to run a simulation for a membrane protein. As per a tutorial, i require a lipid bilayer and some (.itp) files for editing manually a toplogy file for the lipid bilayer. Question is how do I choose the appropriate lipid bilayer and its subsequent (.itp) file? 

That depends on what you are modelling and what you are hoping to observe. There's no substitute for knowledge and learning about the biochemical system of interest, and how other people have approached similar problems, and what they learned.

> Also, what are the required necessary things to be edited. I intend to use teh OPLS-AA force field to represent my protein

That sounds like you are pre-supposing the use of a particular tool. A better approach is to look at published studies similar to the one you propose, to learn from their apparent successes and failures, and to choose tools and methods accordingly.

Having chosen tools and methods, it is certain that you will need to spend time reading tutorials, documentation, published articles and asking questions of experts. Indeed, if you can't do this, then you should probably revisit those chocies of tools and methods, or even the proposed study.

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