From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Fri Nov 11 2011 - 06:21:38 CST
Dear Marco and Bin,
Looking at the code - the angles is between the planes 1-2-3 and 2-3-4. I
presume also that when you ask about the restriction, you're referring to
CHARMM-formatted parameters files for use in namd. Indeed there is a
restriction, the order of the atoms must match the order they are found in
the IMPROPER entry of the psf file. If I remember correctly, the convention
is that the central atom is in position A in A-B-C-D.
Cheers,
Johan
------------------------------------------------------------------------------------------------------
Johan Strumpfer: johanstr_at_ks.uiuc.edu
www.ks.uiuc.edu/~johanstr <http://www.ks.uiuc.edu/%7Ejohanstr>
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA
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On Fri, Nov 11, 2011 at 3:34 AM, Marco Sant <labicia_at_yahoo.it> wrote:
> Dear all,
> if in the parameters file I specify an improper angle
> as formed by the following atoms:
>
> A-B-C-D
>
> does it mean that the improper angle is the one
> between the planes A-B-C and B-C-D ??
>
> I guess so looking at the meaning of dihedral angle,
> A-B-C-D, as angle between planes A-B-C and B-C-D,
> and seeing in the source code that dihedrals and impropers
> have a similar approach.
>
> Still, I have to answer to a referee for the publication
> of an article and I need a RELIABLE answer.
> I apologize if this is explained somewhere and it is
> just me that cannot find it!
>
> Secondary aspect. In an improper angle there
> is always a central atom to which other three atoms
> are connected.
> In the lower schema the central atom is numbered as 1.
>
> 3
> |
> 1
> / \
> 2 4
>
> Is there a restriction, when I specify the potential for the
> improper A-B-C-D, to which position the central atom
> should have?
> For example, in my calculations I specify the improper
> of the above schema as: 2-3-1-4.
> In other words: should the central atom 1,
> appear in position B and C, or in position A and D,
> when specifying A-B-C-D improper?
>
> Thanks a lot,
> Marco and Bin
>
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