[AMBER] sum of charges from parm file

From: Lenka <Vellryba.seznam.cz>
Date: Wed, 01 Apr 2020 00:27:36 +0200 (CEST)


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

 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

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Received on Tue Mar 31 2020 - 15:30:02 PDT
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