[gmx-users] protein simulation w/ urea + water

[E. Nihal Korkmaz]

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:   korkmaz at wisc.edu
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