Re: about angles in coordination complexes

From: luca belmonte (lucabelmonte_at_gmail.com)
Date: Mon Jan 26 2015 - 10:28:17 CST

Yes, in the QM calculations I have all of them, but I did not mapped them
into the par file.

What I have done is to map everything related to the methanethiol group of
the cysteine residue of the top/par files but I did not mapped any angle
between the sulphurs of different cysteines (the S-M2+-S angle you said).

Could you please provide me any example, keyword or manual reference to do
that?

2015-01-26 17:20 GMT+01:00 Jrme Hnin <jerome.henin_at_ibpc.fr>:

> 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 Jrme Hnin <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
>>
>
>

-- 
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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