From: luca belmonte (lucabelmonte_at_gmail.com)
Date: Mon Jan 26 2015 - 10:02:27 CST
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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