AMBER Archive (2006)

Subject: Re: AMBER: heme improper torsions

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Mon Jan 16 2006 - 03:50:50 CST

You are loading a prepin file so you should check whether you really
need those impropers...

Since you are taking the file from the amber database, I believe that
the prep file for the heme includes only required impropers... but in
general the prep files contain more impropers than those actually
required ...

Using the definition of impropers (see amber manual) and your chemical
intuition, you should be able to decide whether a certain improper is
required or not. You can also easily check the influence of one or other
improper by running short minimizations (or short MD) with the system
with and without a certain improper.

Hope this helps
vlad

P.S. I believe a better choice than loading prep files is to load mol2
or off files and to define the necessary impropers in the frcmod file ....

nkyx_at_sohu.com wrote:

> Hi all,
>
> I am new user to Amber. When I used xleap to prepare a system
> containing HEME, it gave me the message enclosed. I used the
> parameters from http://pharmacy.man.ac.uk/amber/.
>
> I don't know whether the old impropers significantly affect the
> simulation result. Could anybody with experience give me some advice?
> Thanks in advance.
>
> nkyx
>
> The message is enclosed.
>
> Building improper torsion parameters.
> old PREP-specified impropers:
> <CYF 439>: -M CA N H
> <CYF 439>: CA +M C O
> <HEM 497>: NA C1A C4A FE
> <HEM 497>: NB C1B C4B FE
> <HEM 497>: NC C1C C4C FE
> <HEM 497>: ND C1D C4D FE
> <HEM 497>: C1A C2A NA CHA
> <HEM 497>: C1B C2B NB CHB
> <HEM 497>: C1C C2C NC CHC
> <HEM 497>: C1D C2D ND CHD
> <HEM 497>: C2A C3A C1A CAA
> <HEM 497>: C2B C3B C1B CMB
> <HEM 497>: C2C C3C C1C CMC
> <HEM 497>: C2D C3D C1D CMD
> <HEM 497>: C3A C4A C2A CMA
> <HEM 497>: C3B C4B C2B CAB
> <HEM 497>: C3C C4C C2C CAC
> <HEM 497>: C3D C4D C2D CAD
> <HEM 497>: C4A NA C3A CHB
> <HEM 497>: C4B NB C3B CHC
> <HEM 497>: C4C NC C3C CHD
> <HEM 497>: C4D ND C3D CHA
> total 1595 improper torsions applied
> 22 improper torsions in old prep form
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> CHIE 1
> NLYS 1
> (no restraint)
>
> ------------------------------------------------------------------------
> 只要提意见就能得大奖！ <http://goto.sohu.com/goto.php3?code=mailadt-ta1>
>
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> 

-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/

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