[gmx-users] Solvating protein

Sai Pooja saipooja at gmail.com
Fri Jul 9 17:28:59 CEST 2010


When I start from a energy minimized protein in vacuum and solvate it using
genbox, the output message says that the protein has zero charge. So I skip
the genion step. I follow this with energy minimization of the solvated
protein followed by restraining the protein and then doing a short mdrun (as
is the usual procedure outlined in most tutorials). However, when I run the
grompp command as the first step for the position restrained md, it runs but
prints a note saying that the system has non-zero charge ~ -  0.9999.

NOTE 2 [file finalnoss.top, line 8070]:
  System has non-zero total charge: -9.999994e-01

I dont understand. Do I need to run the genion step anyway or is it okay to
continue with this system?


Quaerendo Invenietis-Seek and you shall discover.

Quaerendo Invenietis-Seek and you shall discover.
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