AMBER Archive (2001)

Subject: Perturbed internal coordinate parameters

From: Michael Jakusch (mjakusch_at_pharma.anbi.ethz.ch)
Date: Wed Sep 26 2001 - 14:40:36 CDT

Dear AMBER users!

I'm trying to set up a system for FEP simulations, but after digging
through all information I could find concerning the correct treatment
of internal coordinates, I'm more and more confused ...

I want to convert GLN to ASN, so I thought of using this topology:

    H H H O H H O H
    | | | // | | || /
-NH-CA-CB-CG-CE -NH-CA-CB-CG-N
    | | | \ ----> | | | \
  O=C H H N-H O=C H HD H-D
    | | | |
               H D

    lambda = 1 lambda = 0

In some source I found that for dummy atoms one should set the force
constants of all dihedrals to zero, but leave the bonds and angles as
they are. In my case this would mean:

BOND
C -HD 340.0 1.090 :=: CT-HC
D -H 434.0 1.010 :=: H -N

ANGL
HD-C -CT 50.0 109.50 :=: CT-CT-HC
HD-C -N 50.0 109.50 :=: C -CT-HC
HD-C -O 35.0 109.50 :=: HC-CT-HC
D -H -D 35.0 120.00 :=: H -N -H
D -H -N 50.0 120.00 :=: C -N -H

However, during the perturbation CG should change from sp3 to sp2
hybridization; as far as I understand, keeping the HD-C-X angles at
109 degree would not allow for the correct planar geometry even at
lambda=0, but rather create a high strain on this atom.

What should I do (in this special case and in general)?

Thanks in advance for your help

Michael 

-- 
Dr. Michael Jakusch

ETH - Swiss Federal Institute of Technology
Departement of Applied Biosciences
Winterthurerstrasse 190
CH-8057 Zürich
Switzerland
Phone: +41.1.635 60 71
Fax:   +41.1.635 68 84
email: michael.jakusch_at_pharma.anbi.ethz.ch