[gmx-users] 2 chain protein itp file

Mark Abraham Mark.Abraham at anu.edu.au
Sun Apr 1 08:05:28 CEST 2012

On 1/04/2012 3:03 PM, Acoot Brett wrote:
> Dear All,
> According to the lysozyme model in the tutorial of *Justin Lemkul *in 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html, 
> I am runing a 2 chain protein complex MD, and the steps are exactly 
> same as in that on-line tutorial  except that I use the 2 chain 
> protein rather than laysozyme. In the preparation steps, GROMACS 
> produces 2 *.itp file,ne for chain A, one for chain B. But in the 
> following steps, I find the 2 *.itp files have never been used by the 
> following command. Thus sometimes I am suspicious for the following 
> steps whether the MD was done only on Chain A or on both Chains.
> Will you please clarify why GROMACS produces the 2 *.itp files but 
> never used them in the following MD steps? Have I done something wrong 
> on my 2 chain protein MD?

See manual 5.7.2 and 

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