AMBER Archive (2002)

Subject: Fw: parameter estimation

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Fri Mar 08 2002 - 03:52:50 CST

----- Original Message -----
From: "Lepsa" <lepsik_at_marilyn.uochb.cas.cz>
To: "Vlad Cojocaru" <Vlad.Cojocaru_at_mpi-bpc.mpg.de>
Sent: Friday, March 08, 2002 8:44 AM
Subject: Re: parameter estimation

> Dear Vlad,
> what you should do to create a modified forcefield file (see plastocyanin
> tutorial on AMBER web page). You derive equilibrium values from
QM-optimized
> fragments or experiments (e.g from Cambridge Structural Database). Force
> constants you can use by analogy, unless you want to go about vibrational
> analysis, which'd be a tough job.
>
> Good luck,
>
> Martin Lepsik
>
>
>
> ----- Original Message -----
> From: "Vlad Cojocaru" <Vlad.Cojocaru_at_mpi-bpc.mpg.de>
> To: <amber_at_heimdal.compchem.ucsf.edu>
> Sent: Thursday, March 07, 2002 7:32 PM
> Subject: parameter estimation
>
>
> > I have a new Rna residue that I have created using RG unit and modifying
> > it according to my needs by assigning the atom types for the new atoms
> > created. If I want to create the parm and coord files leap is telling me
> > that it could not find several bond, angle and torsion parameters.
> > Is it correct to assign this parameters with the values obtained by
> > measuring them with measureGeom command?
> >
> > --
> > Vlad Cojocaru
> > Max Planck Institut for Biophysical Chemistry
> > Deparment: 060
> > Am Fassberg 11, 37077 Goettingen, Germany
> > tel: ++49-551-201.1389
> > e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
> > Home Address: Gutenbergstrasse 26/8
> > 37075 Goettingen, Germany
> > Home tel. number: ++49-551-9963204
> > Mobile: ++49-179-6851586
> > alternative email: johhnny_ar_at_yahoo.com
> >
>