Hi,
I am to simulate protein in 0.15M NaCl. It is a membrane protein so I build
the membrane in Charmm and generate files for Amber.
Despite the fact I select 0.15M NaCl, I get this message in the min_mdout
file:
Sum of charges from parm topology file = 0.00000000
Forcing neutrality...
Shouldn't there be a charge present in the parm file if the ions add to 150
mM NaCl? There are ions present in the generated pdb.
My second question is, if I select the charge will the Amber PME calculation
neutralize the charge anyway? I was under the impression that this happens
so how can you run a simulation at 0.15M?
Thank you for the explanation
L.
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Received on Tue Mar 31 2020 - 15:30:02 PDT
