AW: about angles in coordination complexes

From: Norman Geist (
Date: Mon Jan 26 2015 - 09:24:39 CST



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: [] Im Auftrag
von luca belmonte
Gesendet: Montag, 26. Januar 2015 15:39
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

       \ /


       / \

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


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

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