From: luca belmonte (lucabelmonte_at_gmail.com)
Date: Mon Jan 26 2015 - 09:28:16 CST
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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