Atila Petrosian wrote:
I want to use define = -DPOSRES_Protein_chain_A for step 1.
is it true?
Not per the topology you posted earlier. Your only option (at this point) for
restraining the protein is -DPOSRES, which restrains all the chains.
If you want to restrain parts of your structure, you will likely need to create
custom posre.itp files for the different chains (or whatever merged combinations
of them) using genrestr and perhaps custom index groups generated by make_ndx.
A trivial example of such a procedure is described in the protein-ligand
tutorial I wrote:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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