AMBER Archive (2008)

Subject: Re: AMBER: Newbie question: partial minimization in implicit solvent

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Nov 12 2008 - 14:47:56 CST

use strong restraints

On Wed, Nov 12, 2008 at 12:48 PM, Jochen Heil <jheil_at_keychem.de> wrote:
> Hi,
>
> I have a protein pdb structure built from X-ray data with hydrogen atoms
> added by some empirical/heuristical method. I want to perform a partial
> optimization using a GB implicit solvent model by constraining the
> positions of certain atoms (defined by groups or geometric criteria).
>
> The obvious solution seems to be to construct an input similar to the
> following (just an example for the optimization of hydrogen sites):
>
> &cntrl
> imin=1, ntb=0, cut=999, igb=1, ibelly=1, bellymask="@H="
> /
>
> However, the manual says (Amber9/10) that GB implicit solvent minimization
> using constraint atoms is currently not possible. On the other hand,
> DOCK6.1
> apparently allows the definition of frozen atoms upon GB minimization
> in the context of amber_score. Is there a workaround for doing this in
> native Amber?
>
> Cheers, Jochen
>
> --
>
> Dipl.-Ing. Jochen Heil
> AG Kast
> Eduard-Zintl-Institut für Anorganische und Physikalische Chemie
> Technische Universität Darmstadt
> Petersenstr. 20, 64287 Darmstadt, Germany
>
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