AMBER Archive (2007)

Subject: Re: AMBER: Problem with leaprc

From: yen li (chem_me2000_at_yahoo.com)
Date: Wed Jul 04 2007 - 07:23:49 CDT

Dear Dr. Case,
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
(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?

I am attaching the corresponding pdb file.

Regards,
Yen

"David A. Case" <case_at_scripps.edu> wrote: On Sun, Jul 01, 2007, yen li wrote:

> (2) I do "desc ff03"

I've never done this, so I'm not sure what to expect. To really know what is
being computed, set up a small molecule, and "dihed" command in rdparm to
print out the dihedrals from the prmtop file. That is what sander and pmemd
really see.

...dac

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