[gmx-users] 2 chain protein itp file

Acoot Brett acootbrett at yahoo.com
Sun Apr 1 07:03:10 CEST 2012

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?

I am looking forward to getting your reply.


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