Problem with iron ion (FE2+)

From: Daniela Rivas (
Date: Mon Aug 24 2015 - 12:51:59 CDT


I'm trying to run a molecular dynamics with Namd with an introduced iron
ion (FE2+) inside the protein, where is suppose to be. I checked my ionized
PDB and PSF and everything was perfect, but when the simulation started I
found that the iron was not in the position where it was supposed to be and
it was touching another atom, which is bad because I can't analyse that.

Any thoughts about what's happening? I've done every step twice and I get
the same result.

Thanks in advance,

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