Ohh.. I had got the AMBER parameters a few days back only from website and didn't care thereafter. Thankyou Dr. Case for the very kind help. Also to help others, please ask web admin to update the amber parameters file from the website.
Best Regards,
Yen
"David A. Case" <case.scripps.edu> wrote:
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 - 06:07:14 PDT
