From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Mon Aug 24 2015 - 13:09:01 CDT
If you 100% confined that Fe2+ ion should be in position in which you
introduced it initially, try to impose restraint to this ion.
Also impose restraints to all counter-ions that you have in system under
consideration, especilay to negatively charged ones.
On 8/24/2015 7:51 PM, Daniela Rivas wrote:
> 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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