AMBER Archive (2009)

Subject: Re: [AMBER] DG improper torsion problem, two missing parameters

From: case (case_at_biomaps.rutgers.edu)
Date: Fri Oct 09 2009 - 06:46:34 CDT

On Fri, Oct 09, 2009, Youn Kyeung Lee wrote:
>
> I checked 'DG.prep' file(from xleap by typing 'saveamberprep DG DG.prep'),
> and I could see there are 8 improper torsions assigned for Guanine.
> ==============================
> IMPROPER
> C4 C8 N9 C1'
> H8 N9 C8 N7
> C6 C4 C5 N7
> C5 N1 C6 O6
> C6 C2 N1 H1
> N2 N1 C2 N3
> C2 H21 N2 H22
> C5 N9 C4 N3
> ==============================

These are really only *likely* improper torsions. If the force field you use
doens't have improper parameters for some set of atoms, then no improper term
will be used.

>
> However when I tried to get prmtop file,
> I got warning messages as below
> ================================================
> ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
> atoms are: N9 C5 C4 N3
> ** Warning: No sp2 improper torsion term for NB-C-CB-CB
> atoms are: N7 C6 C5 C4
> ================================================

This is OK, and expected. It is not required that all potential impropers
actually be used, and the Amber force fields don't use all possible
combinations for purines.

...dac

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