From: luca belmonte (lucabelmonte_at_gmail.com)
Date: Mon Jan 26 2015 - 08:39:17 CST
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
The complexes are "rubredoxin" likes, and you can look at coordination
sphere as follows:
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,
-- Luca Belmonte, PhD
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