Re: constructing a topology entry for hexadecane

From: Victor Ovchinnikov (ovchinnv_at_mit.edu)
Date: Fri Jun 29 2007 - 10:37:19 CDT

The description of the CHARMM topology file can be found in the CHARMM
site http://www.charmm.org/document/Charmm/c32b2/rtop.html

If you feel like reading the original CHARMM paper (Brooks et al 1983,
JCC, 4,187) (which I think is a good thing for NAMD users using CHARMM
fields), you will find the following information:

The entries labeled IC (internal coordinates) contain all of the
information required to build the coordinates of the residue from bond
lengths, angles and dihedrals. A * preceding the third atom name
indicates that this is an improper dihedral angle internal coordinate.
The zeros in this table are filled with values that correspond to
minimum energy geometries found in the parameter file, except for the
middle column (dihedral angle); any nonzero value is not replaced.

Victor

On Thu, 2007-06-28 at 19:25 -0400, Adam Fraser wrote:
> I was hoping someone could explain to me why it is the Internal
> Coordinate (IC) statements in top_all27_lipid contain only dihedral
> data and have 0.0 for all 4 other values.
>
> eg: in Hexane these are the IC statements
>
> ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00
> ic c2 c3 c4 c5 0.00 0.00 180.0 0.00 0.00
> ic c3 c4 c5 c6 0.00 0.00 180.0 0.00 0.00
> ic c3 c2 c1 h11 0.00 0.00 180.0 0.00 0.00
> ic h11 c2 *c1 h12 0.00 0.00 120.0 0.00 0.00
> ic h11 c2 *c1 h13 0.00 0.00 240.0 0.00 0.00
> ic c1 c3 *c2 h21 0.00 0.00 120.0 0.00 0.00
> ic c1 c3 *c2 h22 0.00 0.00 240.0 0.00 0.00
> ic c2 c4 *c3 h31 0.00 0.00 120.0 0.00 0.00
> ic c2 c4 *c3 h32 0.00 0.00 240.0 0.00 0.00
> ic c3 c5 *c4 h41 0.00 0.00 120.0 0.00 0.00
> ic c3 c5 *c4 h42 0.00 0.00 240.0 0.00 0.00
> ic c4 c6 *c5 h51 0.00 0.00 120.0 0.00 0.00
> ic c4 c6 *c5 h52 0.00 0.00 240.0 0.00 0.00
> ic c4 c5 c6 h61 0.00 0.00 180.0 0.00 0.00
> ic h61 c5 *c6 h62 0.00 0.00 120.0 0.00 0.00
> ic h61 c5 *c6 h63 0.00 0.00 240.0 0.00 0.00
>
> I'm constructing a topology file for Hexadecane and was hoping to
> simply extend this Hexane residue.
>
> Any help provided would be greatly appreciated.
>
> Best,
> Adam

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