[gmx-users] Residue name

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 5 19:19:36 CET 2009

Dinesh Pinisetty wrote:
> Hello,
>           I am trying to run a simulation using a surfactant and acetone molecules. I have residue name of "ACT" for my acetone molecule. When I perform energyminimization of my structure file, I end up having residue name of my surfactant all through the structure file. I have acetone.itp and surfactant.itp added to my directory and a path provided in my topology file. I am also using ffG53a5.itp file provided in GROMACS. Can anyone let me know possible mistakes. I was also wondering if there is any other place where I got to add the residue name of the acetone molecule. I did not have any problem when I ran my simulations with surfactant and water moleucle. But for water molecules, I used flexspc.itp provided in GROMACS. 

I don't understand what you mean by "having residue name of my surfactant all 
through the structure file."  Can you post a snippet of your structure file to 
illustrate what you mean?

As for acetone, you don't need to add a residue name anywhere, just #include 
"acetone.itp" in your topology, and make sure the [ molecules ] directive of 
your .top contains the appropriate number of ACT molecules.


> Any suggestions are greatly appreciated.
> Thanking You,
> Sincerely,
> Dinesh.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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