[gmx-users] defining impropers necessary?

Justin Lemkul jalemkul at vt.edu
Wed Jul 17 17:51:55 CEST 2013

On 7/17/13 11:39 AM, gromacs query wrote:
> Dear Justin,
> 1) I can understand the improper for stereocenters (chiral) easily but with

OPLS doesn't use impropers for chiral centers.

> bonds I am confused (I have tried to explain below please let me know if I
> have defined impropers correctly for peptide to keep it planar).
>   H1     O          H3
>      \      I          /
>   --C1---C--N---C2--
>      /         I      \
>    H2       H      H4

OK, funky text drawing :)  But it looks like you've got an amide flanked by two 
methylene groups as the repeat unit.

> So I think improper (being zero) to keep peptide planar should be defined
> (and sufficiently) as: O C N C1
> and dihedral should be which is simple as: O C N H
> But it confuses me, why one needs to define improper for peptide. If I just
> keep dihedral angle strict (high force constant) then it will make peptide
> freezed! so it will remain planar.

The OPLS approach for amides is to define normal dihedrals as well as impropers. 
  Keep in mind that rotations about a bond and out-of-plane bending are 
different types of motion.  I suppose you could achieve what you're thinking of 
by very strong force constants for the dihedrals, but I would wonder if you're 
then throwing the balance of 1-4 interactions (especially charges) out of whack.

> 2) Also, I am not sure whether OPLS needs this peptide bond to be defined
> with improper, someone have experienced this please suggest?

All the amino acids in the aminoacids.rtp file specify impropers centered on the 
C and N atoms of the peptide bond.  I would stick with that approach.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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