AMBER Archive (2007)

Subject: Re: AMBER: Specific/Non-specific dihedral issue in Amber

From: Narayanan Veeraraghavan (narayanan.veeraraghavan_at_gmail.com)
Date: Mon Jul 09 2007 - 13:02:38 CDT

For example: The following entry for cytosine (RC) involving atoms O4'
 C4' C3' H3' (atom types:OS CT CT H1)

      27: 0.250 0.00 1.0 O4' C4' C3' H3' (10,8,25,26)
     28: 0.156 0.00 3.0 O4' C4' C3' H3' (10,8,25,26)

Again for H4' C4' C3' O3' (atom types: H1 CT CT OS)
      34: 0.250 0.00 1.0 H4' C4' C3' O3' (9,8,25,31)
     35: 0.156 0.00 3.0 H4' C4' C3' O3' (9,8,25,31)

Numbers in brackets indicates the atom numbers implying that we are
talking about the exact same atoms.

In both the instances above, the parm99.dat contains a single entry
for specifically H1-CT-CT-OS:
H1-CT-CT-OS 1 0.25 0.0 1. Junmei et al, 1999

The other non-specific entry in parm99.dat matching H1-CT-CT-OS is X -CT-CT-X :
X -CT-CT-X 9 1.40 0.0 3. JCC,7,(1986),230

So, this lead me to ask - why is the non-specific dihedral included
when we have already found a match to a specific dihedral.

Thanks,
Narayanan

On 7/9/07, David A. Case <case_at_scripps.edu> wrote:
> On Mon, Jul 09, 2007, Narayanan Veeraraghavan wrote:
>
> > I was looking up the dihedral dump from rdparms and I see that in
> > addition to specific dihedrals, non-specific dihedrals are also
> > included. For example: H1-CT-CT-OS as well as X-CT-CT-X
> >
> > I would have thought that if a specific dihedral is available, the
> > non-specific dihedrals should be ignored.
>
> This is correct. Can you provide a small example of what you are seeing?
>
> ...dac
>
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