Re: Problem with iron ion (FE2+)

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Aug 24 2015 - 14:17:20 CDT

Hi Daniela,

I've usually seen metal ions inside proteins treated as being covalently
linked to their natural protein interaction partners. Either it is done
explicitly in building up the topology (heme is the classic example of
this), or if no other parameters are available, NAMD extrabonds are used
to mimic the interactions the ion would have with its surroundings
(usually with force constants and equilibrium lengths in line with what
was seen in the crystal structure). Harmonic restraints are sometimes
unsuitable, especially if you expect the protein to move, as the
harmonic restraints won't move with a diffusing protein, causing the ion
to drift within the protein.

-Josh Vermaas

On 08/24/2015 01:40 PM, Branko wrote:
> 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
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_namd_2.9_ug_node27.html&d=AwMDaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=_iaEoQjQ5EXnJSwTmnVyAZQ3CIZUkE2n0RJVT0n7trY&s=R27mnEy-4TAoHw-mWIWfS0v6EGB2bYAy1C5YcMaU5XU&e=>
>>
>> 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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