Thank you very much Jason!
On 4/19/11, Jason Swails <jason.swails.gmail.com> wrote:
> 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
>>
>> _______________________________________________
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>> 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
>
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Received on Tue Apr 19 2011 - 12:00:02 PDT
