From: Daniela Rivas (dani.rivas.r_at_gmail.com)
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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