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.
Cheers,
Acoot
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