Re: [AMBER] How to define trivalent Sulphur ligand atom

From: Jason Swails <>
Date: Mon, 8 Nov 2010 11:18:42 -0500

Amber (and typically force fields in general), have no concept of bond
order, or any of the other mnemonics we use to describe bonding patterns
(i.e. "expanded octet", etc.). They only see the topology of the system and
various other nonbonded parameters, such as the charge or dispersion radii.
The mnemonics we use simply help us predict relative bond strengths,
lengths, etc., but those manifest themselves in the force field through the
actual parameters.

Techniques to develop force field parameters for these unusual systems
generally rest on drawing on results from experiment or high level quantum
mechanical calculations to extract equilibrium geometries, various
frequencies (from which you can derive force constants) and charges.

(I'm also not exactly sure what the problem is with having a sulfur atom
only bonded to 3 different objects... carbonyl carbons are the same, etc.
Am I missing something?)

Hope this helps,

On Mon, Nov 8, 2010 at 3:00 AM, Mannan <> wrote:

> Hi,
> I have a different protein with two zinc atoms and a bound ligand in PDB.
> where the Suphur atom (present in the ligand) is covalently bound with two
> Zinc
> atoms,
> How to treat such atoms,
> Even if I treat the Suplhur as deprotonated, the valency of the Suplhur
> atom is
> three.
> Should I tweak some where else.
> I have two such proteins to deal with, while the related structure paper
> did not
> mention anything about that
> Any Help will be greatly appreciated
> Mannan
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Nov 08 2010 - 08:30:06 PST
Custom Search