On Wed, Jul 04, 2007, yen li wrote:
> As suggested I have done 'rdparm->dihedral' analysis for a tripeptide. Below
> I am giving the first two non hydrogen dihedral details. (Using leaprc.ff03)
>
> 113: 2.500 3.14 2.0 :1.O :1.C :2.N :2.CA (19,18,20,22)
> 114: 0.778 3.14 1.0 :1.C :2.N :2.CA :2.CB (18,20,22,24)
> E 115: 0.066 3.14 2.0 :1.C :2.N :2.CA :2.CB (18,20,22,24)
> E 116: 0.056 0.00 3.0 :1.C :2.N :2.CA :2.CB (18,20,22,24)
> E 117: 0.000 3.14 4.0 :1.C :2.N :2.CA :2.CB (18,20,22,24)
>
>
> (a) first dihedral is O -C -N -CT or CT-N -C -O, I am unable to find such
> dihed parameters in parm99.dat or frcmod.ff03
This is a wild-card dihedral: look for X -C -N -X in parm99.dat
> (b) 2nd, 3rd, 4th dihedrals are C -N -CT-CT but the above parameters are of
> CT-CT-C -N of frcmod.ff03.
>
> Is this a bug?
Have you applied bugfix.5? Here is what I get for your peptide:
113: 2.500 3.14 2.0 :1.O :1.C :2.N :2.CA (19,18,20,22)
114: 0.354 3.14 1.0 :1.C :2.N :2.CA :2.CB (18,20,22,24)
E 115: 0.884 3.14 2.0 :1.C :2.N :2.CA :2.CB (18,20,22,24)
E 116: 0.227 3.14 3.0 :1.C :2.N :2.CA :2.CB (18,20,22,24)
E 117: 0.000 0.00 4.0 :1.C :2.N :2.CA :2.CB (18,20,22,24)
which matches what is in frcmod.ff03.
To all amber users: it is *essential* to apply bugfix.5 if you are planning
to use the ff03 force field.
...hope this helps....dac
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Received on Sun Jul 08 2007 - 06:07:12 PDT
