Liu Shiyong wrote:
I tried to make energy groups from the "output" (*.gro) from pdb2gmx.
>
Found 0 atoms with chain identifier B
Group is empty
>
Found 0 atoms with chain identifier A
Group is empty
That means no chain id information in *.gro, but I have to define the
energy groups according to chain id .
Then either specify a .pdb file as the pdb2gmx output, or instead of using chain
identifiers, specify the residues within each group. For example, if chain A is
residues 1-300, then at the make_ndx prompt, type r 1-300.
-Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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