Hello,
Your analysis is correct. The numbers to the right are the atom numbers.
The numbers to the left are the barrier height, phase shift, and
periodicity, respectively. Note that the barrier height is already divided
by the multiplicity factor (or however it's described in
http://ambermd.org/formats.html). Note that dihedral indexing/assignment
can get quite complicated depending on what terms are present in your force
field.
I have seen 2 prmtop files that, when diffed give a large number of
differences, but yield the same energies in sander. The bottom line is, I
think, that for different force fields, you can't expect the dihedral terms
to relate to one another in such a direct way.
As a demonstration of what I was talking about earlier, try running the
following script through tleap with ff99SB (or ff10):
sys = sequence {ACE ALA ALA ALA NME}
sys2 = copy sys
saveamberparm sys parm1 crd1
saveamberparm ssy2 parm2 crd2
If you diff parm1 and parm2, you'll see substantial differences, but they
will yield the same energy.
HTH,
Jason
On Tue, Apr 19, 2011 at 9:57 AM, david condon <dec986.gmail.com> wrote:
> Hi All,
>
> I am checking dihedral parameters using rdparm for my LNA
> tetranucleotide, and here are some results from rdparm's dihedral
> command:
>
> for force field A:
> 269: 0.000 0.00 2.0 :1.C2' :1.C1' :1.N1 :1.C2 (24,8,10,20)
> 357: 0.000 0.00 2.0 :2.O4' :2.C1' :2.N9 :2.C4 (39,40,42,55)
> 443: 0.000 0.00 2.0 :3.O4' :3.C1' :3.N9 :3.C4 (73,74,76,89)
> 512: 0.000 0.00 2.0 :4.C2' :4.C1' :4.N1 :4.C2
> (123,108,110,119)
>
> for force field B:
> 251: 0.000 0.00 2.0 :1.C2 :1.N1 :1.C1' :1.O4' (20,10,8,7)
> 367: 0.000 0.00 2.0 :2.O4' :2.C1' :2.N9 :2.C4 (39,40,42,55)
> 458: 0.000 0.00 2.0 :3.O4' :3.C1' :3.N9 :3.C4 (73,74,76,89)
> 514: 0.000 0.00 2.0 :4.C2 :4.N1 :4.C1' :4.O4'
> (119,110,108,107)
>
> The two molecules are identical except for the force fields.
>
> Unfortunately the AMBER manual said nothing about how to read the
> output. I thought that the four numbers at right were atom #s, but
> the two molecules are identical. My question is, what are the 3
> numbers on the left? I thought they were cosine terms but then the
> different force fields are giving vastly different results, as they
> were designed to.
>
> What are the 4 numbers on the right?
>
> thanks in advance for your time,
> -Dave
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 19 2011 - 11:00:03 PDT
