From: Daniela Rivas (dani.rivas.r_at_gmail.com)
Date: Mon Aug 24 2015 - 13:16:15 CDT
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>:
> 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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