Thanks very much for reply. You meant " impropers will be applied to all matching sites and can't be applied in the united atom forcefield". How can you add impropers to out-plane chiral and at the same time insure the consistance between torsional energy profile and quantum chemistry calculation ? Did you think about the improper dihedral energy when deducing the proper dihedral parameters?
Regards
Shanshan Qin
> -----Original Message-----
> From: Bill Ross <ross.cgl.ucsf.edu>
> Date: Tue, 22 Jul 2008 21:28:07 -0700 (PDT)
> To: amber.scripps.edu
> Subject: Re: AMBER: improper dihedral in ff03 united atom forcefield
> > will somebody give me some explanation?
>
> Note that nonplanar impropers cannot be used with the Leap programs.
> As posted earlier today:
>
> Subject: Re: AMBER: amber ff and how it deals with out-plane chiral C
> From: Bill Ross (ross_at_cgl.ucsf.edu)
> Date: Tue Jul 22 2008 - 16:44:36 CDT
>
> Before Leap was developed, improper dihedrals were specified by
> listing atoms in the residue definitions. This allowed the order
> of atoms to be uniquely specified in each case, so that for the
> non-planar impropers in the united atom force field, the direction
> of the offset from the plane could be specified.
>
>
> With Leap, the decision was made to have impropers be applied just
> like bonds, angles and torsions: by finding topologically appropriate
> groups of atoms and looking for parameters for them. (The main
> difference is that improper parameters for each group are not required.)
> This eliminated the step of setting the sense by specifying the order
> of the atoms. (It also implies that impropers will be applied to all
> matching sites.)
>
>
> Thus if a non-planar improper is specified, the order of the atoms
> surrounding the central one will be chosen on the basis of alphabetical
> order (I forget if by atom name or type), not chemical context. Finding
> a solution for the united atom force fields was postponed indefinitely
> since these weren't used much. I was the one who discovered and debugged
> the problem, while preparing the original version of leap for release.
>
>
> Bill
>
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Received on Sun Jul 27 2008 - 06:07:03 PDT
