Re: about angles in coordination complexes

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Jan 26 2015 - 10:20:37 CST

What I said was very generic. Now looking at the specific arrangement, it
should be possible to reliably enforce a tetrahedral shape with 6 S-Mg-S
angle potentials. Do you have those in your model? If yes maybe there's a
problem with them.

Jerome

On 26 January 2015 at 17:02, luca belmonte <lucabelmonte_at_gmail.com> wrote:

> Hi Jerome,
>
> Thank you for the reply.
>
> At the very beginning of the story I was wondering to do as you suggest.
> But then I encountered some difficulties. Probably I lack the correct
> keyword to map the dihedral angle between different residues.
>
> Do you have some hint?
>
> Thank you,
> Luca
>
> 2015-01-26 16:56 GMT+01:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
>
>> Hi Luca,
>>
>> > These complexes were previously parameterized with GAMESS US, results
>> of its jobs mapped (to the top and par files)
>>
>> You didn't say what exactly they were mapped to, but your results
>> indicate that the empirical description you have now is not sufficient to
>> describe the geometric constraints around your metal center.
>>
>> You probably need more angle/dihedral/improper dihedral terms. I would
>> include them in the top/par files rather than extraBonds, because they will
>> be an essential part of your custom force field.
>>
>> Jerome
>>
>>
>> On 26 January 2015 at 16:28, luca belmonte <lucabelmonte_at_gmail.com>
>> wrote:
>>
>>> Thank you for the hint!
>>>
>>> Best,
>>> Luca
>>>
>>> 2015-01-26 16:24 GMT+01:00 Norman Geist <norman.geist_at_uni-greifswald.de>
>>> :
>>>
>>>> Hi,
>>>>
>>>>
>>>>
>>>> I think you are less interested in fixing or positional harmonic
>>>> restraints, rather than in defining additional bonds/angles/dihedral to
>>>> maintain your conformation. this can be done quite easy using the
>>>> “ExtraBonds” interface of NAMD. Please find details in the manual.
>>>>
>>>>
>>>>
>>>> Norman Geist.
>>>>
>>>>
>>>>
>>>> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
>>>> Auftrag von *luca belmonte
>>>> *Gesendet:* Montag, 26. Januar 2015 15:39
>>>> *An:* namd-l_at_ks.uiuc.edu
>>>> *Betreff:* namd-l: about angles in coordination complexes
>>>>
>>>>
>>>>
>>>> Dear Namd users,
>>>>
>>>>
>>>>
>>>> I am pretty new to this mail list, so... nice to meet you.
>>>>
>>>>
>>>>
>>>> Let me introduce briefly the target. I want to simulate several small
>>>> complexes made of small peptides. In these peptides cysteines always
>>>> coordinate a transition metal dication (M2+). The purpose is to have a
>>>> guess of the stability of the complexes by mean of internal energy
>>>> estimation.
>>>>
>>>>
>>>>
>>>> The complexes are "rubredoxin" likes, and you can look at coordination
>>>> sphere as follows:
>>>>
>>>>
>>>>
>>>> Cys Cys
>>>>
>>>> \ /
>>>>
>>>> M2+
>>>>
>>>> / \
>>>>
>>>> Cys Cys
>>>>
>>>>
>>>>
>>>> All the complexes on which I am working on have tetrahedral
>>>> coordination shapes, in which the M2+ is in the middle of the cage, while
>>>> cysteines sulphurs are at vertexes.
>>>>
>>>> These complexes were previously parameterized with GAMESS US, results
>>>> of its jobs mapped (to the top and par files) and till know everything is
>>>> fine.
>>>>
>>>>
>>>>
>>>> Now comes the problem. When I look at the shape of the coordination
>>>> complex, after the minimization, I expect to see a tetrahedral
>>>> coordination, but the result is a non common shape in which the M2+ pop out
>>>> from the coordination plane.
>>>>
>>>>
>>>>
>>>> To address this issue I was wondering to fix the sulphur atoms
>>>> positions around the cluster using fixedAtoms, but I am scared that this
>>>> approach can affect calculations, providing wrong energy values. Do you
>>>> think so? Do you have another strategy to overcome this problem?
>>>>
>>>>
>>>>
>>>> Any hint is welcome,
>>>>
>>>> Thank you in advance,
>>>>
>>>>
>>>>
>>>> Best regards,
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> Luca Belmonte, PhD
>>>>
>>>
>>>
>>>
>>> --
>>> Luca Belmonte, PhD
>>>
>>> CIBIO - Center for Integrative Biology
>>> University of Trento
>>>
>>> Phone: +39 0461 28 53 41
>>> Mobile: +39 328 45 81 762
>>>
>>
>>
>
>
> --
> Luca Belmonte, PhD
>
> CIBIO - Center for Integrative Biology
> University of Trento
>
> Phone: +39 0461 28 53 41
> Mobile: +39 328 45 81 762
>

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