Dear all, I am trying to simulate a protein in urea solution. I used *genbox -cp protein_in_box.gro -cs urea+h2o.gro -o out.gro -p topology* but the resulting topology doesn't contain any information on urea nor the atoms of urea. I also tried adding ureas on the protein with *-ci urea_single.gro -nmol some_number* option of genbox, that didn't give me the correct topology either.
How should i create the correct topology? Thanks, Best regards, -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu
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