On 10/07/2010 1:28 AM, Sai Pooja wrote:
Hi,
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?
I'd believe grompp before genbox. Surely you know already what is in
your system, and thus its total charge. You should already know the
protonation state of all of your relevant protein residues, because you
made choices for them with pdb2gmx.
Mark
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.
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Quaerendo Invenietis-Seek and you shall discover.
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