From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Jan 26 2015 - 09:56:07 CST
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
>
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