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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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