From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Mon Aug 24 2015 - 13:40:17 CDT
Daniela,
I suppose that your ion is not bounded to protein, but you initially
asked how to preclude movement of this ion. - probably toward solvent.
Try to read what kind of restraints NAMD offer and to conclude which one
is most suitable for your system. I suppose that harmonic restraint or
extra bond will be most suitable. Also, if use harmonic restraint, in
few separate short simulations you can find most suitable 'force value'
with which you restraint ion
Branko
On 8/24/2015 8:16 PM, Daniela Rivas wrote:
> Hi Branko,
>
> What kind of restraint?
> Also, I forgot to mention that the iron ion is not bonded to the
> protein, it's just interacting with the surrounding residues. So, I
> want it to move during the simulation, that's what I want to look at.
>
> Thanks,
> Daniela.
>
> 2015-08-24 15:09 GMT-03:00 Branko <bdrakuli_at_chem.bg.ac.rs
> <mailto:bdrakuli_at_chem.bg.ac.rs>>:
>
> Daniela,
>
> If you 100% confined that Fe2+ ion should be in position in which
> you introduced it initially, try to impose restraint to this ion.
>
> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node27.html
>
> Also impose restraints to all counter-ions that you have in system
> under consideration, especilay to negatively charged ones.
>
> Branko
>
>
>
>
>
>
> On 8/24/2015 7:51 PM, Daniela Rivas wrote:
>
> Hi,
>
> 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,
> Daniela.
>
>
>
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