AMBER Archive (2007)

Subject: Re: AMBER: Problem with leaprc

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 04 2007 - 11:15:39 CDT

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_at_O :1_at_C :2_at_N :2_at_CA (19,18,20,22)
> 114: 0.778 3.14 1.0 :1_at_C :2_at_N :2_at_CA :2_at_CB (18,20,22,24)
> E 115: 0.066 3.14 2.0 :1_at_C :2_at_N :2_at_CA :2_at_CB (18,20,22,24)
> E 116: 0.056 0.00 3.0 :1_at_C :2_at_N :2_at_CA :2_at_CB (18,20,22,24)
> E 117: 0.000 3.14 4.0 :1_at_C :2_at_N :2_at_CA :2_at_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_at_O :1_at_C :2_at_N :2_at_CA (19,18,20,22)
     114: 0.354 3.14 1.0 :1_at_C :2_at_N :2_at_CA :2_at_CB (18,20,22,24)
E 115: 0.884 3.14 2.0 :1_at_C :2_at_N :2_at_CA :2_at_CB (18,20,22,24)
E 116: 0.227 3.14 3.0 :1_at_C :2_at_N :2_at_CA :2_at_CB (18,20,22,24)
E 117: 0.000 0.00 4.0 :1_at_C :2_at_N :2_at_CA :2_at_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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