Re: constructing a topology entry for hexadecane

From: Adam Fraser (adam.n.fraser_at_gmail.com)
Date: Fri Jun 29 2007 - 08:31:57 CDT

I wonder then if anyone knows someplace where I can find a complete topology
file for hydrocarbons.

Thanks for the heads up Aaron.

-Adam

On 6/28/07, Aaron Oakley <oakley_at_rsc.anu.edu.au> wrote:
>
> Its because the folks with put together the file haven't bothered to
> put in the
> rest of the details (angles and bond lengths).
>
> aaron++
>
>
> On 29/06/2007, at 9:25 AM, 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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