AMBER Archive (2007)

Subject: Fwd: AMBER: Improper angle by Antechamber

From: Pavan G (pavanamber_at_gmail.com)
Date: Tue Jan 30 2007 - 12:46:34 CST

Dear Dr. Wang,

Thanks for your mail. I understand (for reasons mentioned in your reply)
that benzene will have (<=) 6 improper angles defined since it is a planar
molecule. Also, the three improper angles identified by antechamber for my
drug did infact involve sets of coplanar molecules. I am surprised I missed
that detail while viewing the drug; and yes there are no other sets of
4-connected-coplanar atoms in the drug. The correspondence has been quite
educational.

Thank you.

Pavan K. Ghatty

Hi, Pavan,
In AMBER, Improper dihedral angle parameters are used to keep plenary
conformations for such as sp2 carbon etc. Although those kind of parameters
can also help to define the chirality of chiral atoms, they may not
necessary be needed (we try to avoid computational cost). Currently, we only
apply improper torsional angles for atoms in a planar conformations. Is it
clear?

All the best

Junmei

---------- Forwarded message ----------
From: Pavan G <pavanamber_at_gmail.com>
Date: Jan 29, 2007 10:05 AM
Subject: Fwd: AMBER: Improper angle by Antechamber
To: jwang_at_encysive.com

Dear Dr. Wang,

Could you please comment on my question?

Thank you

---------- Forwarded message ----------
Hello all,

I am trying to parameterize a drug and I used antechamber to obtain the
prepin file. The code found three improper angles [pictures attached. In
JPEG format and virus-free]. How do I ensure that these are the only three
improper angles in the system? Why can't atoms C19-C21-C18-C20 or
C20-C15-C24-C19 form an improper angle? I understand that improper angles
confine geometry and sometimes determine the chirality of the central atom.

Thank you.

Pavan

---------------------------------------

Since the early days of the 80's, Amber force fields have not included
improper torsions at around the common atoms of fused aromatic rings. (If I

am reading your figures correctly, those the the terms of atoms
C19-C21-C18-C20 and C20-C15-C24-C19 you list above.) Antechamber/GAFF
follows this tradition. Vibrational analyses of indole and purines
suggested
that these impropers were not needed, but you might want to investigate that
again yourself.

(Junmei may have some comments here...there might have been further
investigations that I am not aware of.)

...regards...dac

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