angles between residues

From: luca belmonte (
Date: Tue Dec 30 2014 - 07:38:14 CST

Dear Namd Developers,

I am new to this mail list and to parameterization of new residues for
CharmmFF, in the following lines I'll try to explain the issue I am facing.

The novel residue I am parameterizing is made of four methanethiols groups
coordinating a transition metal dication. I have all the Quantum Mechanical
parameters (stretch, angle, torsional angle) from previous GAMESS ran.

It seems to work properly with the exception that the coordination sphere
changes its shape from tetrahedral to a not defined shape, in which the
metal center seems to pop out from its original position. Since I am
interested in how this small molecule evolve in time (and internal energy)
I am scared that this can affect my MDs.

Is there a way to keep the angles between these groups constant during
simulation in order to better simulate the correct coordination
arrangement? Could you please suggest a keyword to search through the
manual, if any?
I'd say that this issue can be addressed by using IC, but I miss how to
define it between different residues.

Apologize if this issue was already discussed on previous post but I really
cannot find it on the archive,
Thank you and happy new year!

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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