Hi Dean,
The very simple answer to your question, is that improper dihedrals are needed when they are necessary. (Not very helpful, huh :) ) Let me elaborate some. In my experience, there are times when improper dihedrals are not needed because proper dihedrals are sufficient for modeling the energetics and the conformations of the atoms in question. (Note that in Amber proper and improper dihedral angles are defined by the same functional form.) Other times the person who has done the parameterization deems it necessary to use impropers. So ultimately, to use or not use impropers often comes down to the individual tastes of the person who created the parameters. I personally feel that impropers are need in selected case to correctly model out-of-plane bending, and there are very few, if any, force fields that do not use them.
Some else who knows better can correct me if I am wrong, but I believe that parmchk reports provides any improper dihedrals if it recognizes that they are present in the molecule's topology. A value of 10.5 kcal/mol is reasonable for an improper dihedral. If you are uncertain, the best way to determine if you need the impropers, or not, is to run some test simulations with and without them - then choose the setup that gives the best results. (However, if the goal is to force the improper dihedrals to be 100% planar, then adding an additional force constant to do so is "probably" okay. What you will miss by doing this is the proper modeling of out-of-plane bending, but I am not sure how well Parm99 models this anyway.)
Hope this helps some.
Cheers,
Karl
----- Original Message -----
From: "Dean Cuebas" <deancuebas.missouristate.edu>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Monday, April 12, 2010 9:30:07 PM
Subject: [AMBER] How do you know when to include improper dihedrals????
Dear amberers,
I guess my question is more to Ross Walker, since he is the one whose
parameterized NAD+ files I am referring to, but I'll accept a clarification
from anyone! :-)
Using the .mol2 file with charges and amber atomtypes for NAD+ with parmchk
and the parm99.dat file, a frcmod file is created that contains improper
dihedrals for the aromatic adenine ring system. Yet, in the frcmod file
provided by Ross Walker, there are no such improper dihedrals specified.
First let me say that I am not implying a mistake on Ross's part, because
I've seen a few other instances where this is the case also.
So my question is, when are the impropers that are supplied in the frcmod
file produced by parmchk not necessary?
For example, I have a compound I am parameterizing that contains planar
amides and planar thioester linkages. Using parmchk with the parm99.dat file
gives me impropers in the frcmod file with for each of these, with a large
force constant of 10.5.
Do I need these specifications for these planar linkages??
How do you decide???
Thanks so very much for your help in advance.
With regards,
Dean
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Received on Thu Apr 15 2010 - 06:30:03 PDT
